Linux Basics

Biostat 203B

Display machine information for reproducibility:

sessionInfo()

R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.2.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Los_Angeles
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] htmlwidgets_1.6.2 compiler_4.3.2    fastmap_1.1.1     cli_3.6.1        
 [5] tools_4.3.2       htmltools_0.5.6   rstudioapi_0.15.0 yaml_2.3.7       
 [9] rmarkdown_2.25    knitr_1.44        jsonlite_1.8.7    xfun_0.40        
[13] digest_0.6.33     rlang_1.1.1       evaluate_0.21    

1 Preface

• This html is rendered from linux.qmd on Linux Ubuntu 22.04 (jammy).

  • Mac users can render linux.qmd directly. Some tools such as tree and locate need to be installed (follow the error messages).

  • Windows users need to install WSL (Windows Subsystem for Linux) to render linux.qmd using Ubuntu. Some tools such as tree and locate need to be installed (follow the error messages).

  • Both Mac and Windows users can also use Docker to render linux.qmd within a Ubuntu container.

• In this lecture, most code chunks are bash commands instead of R code.

2 Why Linux

Linux is the most common platform for scientific computing and deployment of data science tools.

• Open source and community support.

• Things break; when they break using Linux, it’s easy to fix.

• Scalability: portable devices (Android, iOS), laptops, servers, clusters, and super computers.

  • E.g. UCLA Hoffmann2 cluster runs on Linux; most machines in cloud (AWS, Azure, GCP) run on Linux.
    

• Cost: it’s free!

3 Distributions of Linux

• Debian/Ubuntu is a popular choice for personal computers.

• RHEL/CentOS is popular on servers. (In December 2020, Red Hat terminated the development of CentOS Linux distribution.)

• UCLA Hoffman2 cluster runs CentOS 7.9.2009 (as of 2023-01-01).

• MacOS was originally derived from Unix/Linux (Darwin kernel). It is POSIX compliant. Most shell commands we review here apply to MacOS terminal as well. Windows/DOS, unfortunately, is a totally different breed.

• Show operating system (OS) type:

echo $OSTYPE

darwin23

• Show distribution/version on Linux:

# only on Linux terminal
cat /etc/*-release

• Show distribution/version on MacOS:

# only on Mac terminal
sw_vers -productVersion

14.2.1

or

# only on Mac terminal
system_profiler SPSoftwareDataType

Software:

    System Software Overview:

      System Version: macOS 14.2.1 (23C71)
      Kernel Version: Darwin 23.2.0
      Boot Volume: Macintosh HD
      Boot Mode: Normal
      Computer Name: FSPH-HZHOU
      User Name: Hua Zhou (huazhou)
      Secure Virtual Memory: Enabled
      System Integrity Protection: Enabled
      Time since boot: 4 days, 16 minutes

4 Linux shells

4.1 Shells

• A shell translates commands to OS instructions.

• Most commonly used shells include bash, csh, tcsh, zsh, etc.

• The default shell in MacOS changed from bash to zsh since MacOS v10.15.

• Sometimes a command and a script does not run simply because it’s written for another shell.

• We mostly use bash shell commands in this class.

• Determine the current shell:

echo $SHELL

/bin/zsh

• List available shells:

cat /etc/shells

# List of acceptable shells for chpass(1).
# Ftpd will not allow users to connect who are not using
# one of these shells.

/bin/bash
/bin/csh
/bin/dash
/bin/ksh
/bin/sh
/bin/tcsh
/bin/zsh

• Change to another shell:

```{bash}
#| eval: false
exec bash -l
```

The -l option indicates it should be a login shell.

• Change your login shell permanently:

chsh -s /bin/bash [USERNAME]

Then log out and log in.

4.2 Command history and bash completion

We can navigate to previous/next commands by the upper and lower keys, or maintain a command history stack using pushd and popd commands.

Bash provides the following standard completion for the Linux users by default. Much less typing errors and time!

• Pathname completion.

• Filename completion.

• Variablename completion: echo $[TAB][TAB].

• Username completion: cd ~[TAB][TAB].

• Hostname completion ssh huazhou@[TAB][TAB].

• It can also be customized to auto-complete other stuff such as options and command’s arguments. Google bash completion for more information.

4.3 man is man’s best friend

Online help for shell commands: man [COMMANDNAME].

# display the first 30 lines of documentation for the ls command
man ls | head -30

LS(1)                       General Commands Manual                      LS(1)

NNAAMMEE
     llss – list directory contents

SSYYNNOOPPSSIISS
     llss [--@@AABBCCFFGGHHIILLOOPPRRSSTTUUWWaabbccddeeffgghhiikkllmmnnooppqqrrssttuuvvwwxxyy11%%,,] [----ccoolloorr=_w_h_e_n]
        [--DD _f_o_r_m_a_t] [_f_i_l_e _._._.]

DDEESSCCRRIIPPTTIIOONN
     For each operand that names a _f_i_l_e of a type other than directory, llss
     displays its name as well as any requested, associated information.  For
     each operand that names a _f_i_l_e of type directory, llss displays the names
     of files contained within that directory, as well as any requested,
     associated information.

     If no operands are given, the contents of the current directory are
     displayed.  If more than one operand is given, non-directory operands are
     displayed first; directory and non-directory operands are sorted
     separately and in lexicographical order.

     The following options are available:

     --@@      Display extended attribute keys and sizes in long (--ll) output.

     --AA      Include directory entries whose names begin with a dot (‘_.’)
             except for _. and _._..  Automatically set for the super-user unless
             --II is specified.

     --BB      Force printing of non-printable characters (as defined by

5 Navigate file system

5.1 Linux directory structure

• Upon log in, user is at his/her home directory.

• tree command (if installed) displays directory structure.
  tree -L levels display levels directories deep.

# display only directories in levels 1, 2 from root directory
tree -d -L 1 /

/
├── Applications
├── Library
├── System
├── Users
├── Volumes
├── bin
├── cores
├── dev
├── etc -> private/etc
├── home -> /System/Volumes/Data/home
├── opt
├── private
├── sbin
├── tmp -> private/tmp
├── usr
└── var -> private/var

17 directories

5.2 Move around the file system

• Where am I? pwd prints absolute path to the current working directory:

pwd

/Users/huazhou/Documents/github.com/ucla-biostat-203b/2024winter/slides/02-linux

• What’s in the current director? ls lists contents of a directory:

ls

Emacs_Reference_Card.pdf
IDRE_Winter_2019_Workshops.pdf
Richard_Stallman_2013.png
Vi_Cheat_Sheet.pdf
autoSim.R
key_authentication_1.png
key_authentication_2.png
linux.html
linux.qmd
linux.rmarkdown
linux_directory_structure.png
linux_filepermission.png
linux_filepermission_oct.png
meanEst.R
redhat_kills_centos.png
runSim.R
screenshot_top.png

• ls -l lists detailed contents of a directory:

ls -l

total 4872
-rw-r--r--  1 huazhou  staff  110345 Mar 10  2023 Emacs_Reference_Card.pdf
-rw-r--r--  1 huazhou  staff  157353 Mar 10  2023 IDRE_Winter_2019_Workshops.pdf
-rw-r--r--  1 huazhou  staff  141962 Mar 10  2023 Richard_Stallman_2013.png
-rw-r--r--  1 huazhou  staff  199492 Mar 10  2023 Vi_Cheat_Sheet.pdf
-rw-r--r--  1 huazhou  staff     258 Mar 10  2023 autoSim.R
-rw-r--r--  1 huazhou  staff  321281 Mar 10  2023 key_authentication_1.png
-rw-r--r--  1 huazhou  staff   96119 Mar 10  2023 key_authentication_2.png
-rw-r--r--  1 huazhou  staff  110025 Mar 10  2023 linux.html
-rw-r--r--  1 huazhou  staff   24084 Dec 27 11:14 linux.qmd
-rw-r--r--  1 huazhou  staff   24221 Dec 27 11:14 linux.rmarkdown
-rw-r--r--  1 huazhou  staff   11662 Mar 10  2023 linux_directory_structure.png
-rw-r--r--  1 huazhou  staff  102188 Mar 10  2023 linux_filepermission.png
-rw-r--r--  1 huazhou  staff   42472 Mar 10  2023 linux_filepermission_oct.png
-rw-r--r--  1 huazhou  staff     381 Mar 10  2023 meanEst.R
-rw-r--r--  1 huazhou  staff  437112 Mar 10  2023 redhat_kills_centos.png
-rw-r--r--  1 huazhou  staff     498 Mar 10  2023 runSim.R
-rw-r--r--  1 huazhou  staff  685657 Mar 10  2023 screenshot_top.png

• ls -al lists all contents of a directory, including those start with . (hidden folders):

ls -al

total 4872
drwxr-xr-x  19 huazhou  staff     608 Dec 27 11:14 .
drwxr-xr-x  23 huazhou  staff     736 Mar 10  2023 ..
-rw-r--r--   1 huazhou  staff  110345 Mar 10  2023 Emacs_Reference_Card.pdf
-rw-r--r--   1 huazhou  staff  157353 Mar 10  2023 IDRE_Winter_2019_Workshops.pdf
-rw-r--r--   1 huazhou  staff  141962 Mar 10  2023 Richard_Stallman_2013.png
-rw-r--r--   1 huazhou  staff  199492 Mar 10  2023 Vi_Cheat_Sheet.pdf
-rw-r--r--   1 huazhou  staff     258 Mar 10  2023 autoSim.R
-rw-r--r--   1 huazhou  staff  321281 Mar 10  2023 key_authentication_1.png
-rw-r--r--   1 huazhou  staff   96119 Mar 10  2023 key_authentication_2.png
-rw-r--r--   1 huazhou  staff  110025 Mar 10  2023 linux.html
-rw-r--r--   1 huazhou  staff   24084 Dec 27 11:14 linux.qmd
-rw-r--r--   1 huazhou  staff   24221 Dec 27 11:14 linux.rmarkdown
-rw-r--r--   1 huazhou  staff   11662 Mar 10  2023 linux_directory_structure.png
-rw-r--r--   1 huazhou  staff  102188 Mar 10  2023 linux_filepermission.png
-rw-r--r--   1 huazhou  staff   42472 Mar 10  2023 linux_filepermission_oct.png
-rw-r--r--   1 huazhou  staff     381 Mar 10  2023 meanEst.R
-rw-r--r--   1 huazhou  staff  437112 Mar 10  2023 redhat_kills_centos.png
-rw-r--r--   1 huazhou  staff     498 Mar 10  2023 runSim.R
-rw-r--r--   1 huazhou  staff  685657 Mar 10  2023 screenshot_top.png

• .. denotes the parent of current working directory.

• . denotes the current working directory.

• ~ denotes user’s home directory.

• / denotes the root directory.

• cd .. changes to parent directory.

• cd or cd ~ changes to home directory.

• cd / changes to root directory.

5.3 File permissions

• chmod g+x file makes a file executable to group members.

• chmod 751 file sets permission rwxr-x--x to a file.

• groups [USERNAME] shows which group(s) a user belongs to:

groups $USER

staff everyone localaccounts _appserverusr admin _appserveradm _lpadmin com.apple.sharepoint.group.2 com.apple.sharepoint.group.3 _appstore _lpoperator _developer _analyticsusers com.apple.access_ftp com.apple.access_screensharing com.apple.access_ssh com.apple.access_remote_ae com.apple.sharepoint.group.1

5.4 Manipulate files and directories

• cp copies file to a new location.

• mv moves file to a new location.

• touch creates a text file; if file already exists, it’s left unchanged.

• rm deletes a file.

• mkdir creates a new directory.

• rmdir deletes an empty directory.

• rm -rf deletes a directory and all contents in that directory (be cautious using the -f option …).

5.5 Find files

• locate locates a file by name (need mlocate program installed):

locate linux.qmd

• find is similar to locate but has more functionalities, e.g., select files by age, size, permissions, …. , and is ubiquitous.

# search within current folder
find linux.qmd

linux.qmd

# search within the parent folder
find .. -name linux.qmd

../02-linux/linux.qmd

• which locates a program (executable file):

which R

/usr/local/bin/R

5.6 Wildcard characters

Wildcard	Matches
?	any single character
*	any character 0 or more times
+	one or more preceding pattern
^	beginning of the line
$	end of the line
[set]	any character in set
[!set]	any character not in set
[a-z]	any lowercase letter
[0-9]	any number (same as [0123456789])

# all png files in current folder
ls -l *.png

-rw-r--r--  1 huazhou  staff  141962 Mar 10  2023 Richard_Stallman_2013.png
-rw-r--r--  1 huazhou  staff  321281 Mar 10  2023 key_authentication_1.png
-rw-r--r--  1 huazhou  staff   96119 Mar 10  2023 key_authentication_2.png
-rw-r--r--  1 huazhou  staff   11662 Mar 10  2023 linux_directory_structure.png
-rw-r--r--  1 huazhou  staff  102188 Mar 10  2023 linux_filepermission.png
-rw-r--r--  1 huazhou  staff   42472 Mar 10  2023 linux_filepermission_oct.png
-rw-r--r--  1 huazhou  staff  437112 Mar 10  2023 redhat_kills_centos.png
-rw-r--r--  1 huazhou  staff  685657 Mar 10  2023 screenshot_top.png

5.7 Regular expression

• Wildcards are examples of regular expressions.

• Regular expressions are a powerful tool to efficiently sift through large amounts of text: record linking, data cleaning, scraping data from website or other data-feed.

• Google regular expressions to learn.

6 Work with text files

6.1 View/peek text files

• cat prints the contents of a file:

cat runSim.R

## parsing command arguments
for (arg in commandArgs(TRUE)) {
  eval(parse(text=arg))
}

## check if a given integer is prime
isPrime = function(n) {
  if (n <= 3) {
    return (TRUE)
  }
  if (any((n %% 2:floor(sqrt(n))) == 0)) {
    return (FALSE)
  }
  return (TRUE)
}

## estimate mean only using observation with prime indices
estMeanPrimes = function (x) {
  n = length(x)
  ind = sapply(1:n, isPrime)
  return (mean(x[ind]))
}

# simulate data
x = rnorm(n)

# estimate mean
estMeanPrimes(x)

• head prints the first 10 lines of a file:

head runSim.R

## parsing command arguments
for (arg in commandArgs(TRUE)) {
  eval(parse(text=arg))
}

## check if a given integer is prime
isPrime = function(n) {
  if (n <= 3) {
    return (TRUE)
  }

head -l prints the first \(l\) lines of a file:

head -15 runSim.R

## parsing command arguments
for (arg in commandArgs(TRUE)) {
  eval(parse(text=arg))
}

## check if a given integer is prime
isPrime = function(n) {
  if (n <= 3) {
    return (TRUE)
  }
  if (any((n %% 2:floor(sqrt(n))) == 0)) {
    return (FALSE)
  }
  return (TRUE)
}

• tail prints the last 10 lines of a file:

tail runSim.R

  n = length(x)
  ind = sapply(1:n, isPrime)
  return (mean(x[ind]))
}

# simulate data
x = rnorm(n)

# estimate mean
estMeanPrimes(x)

tail -l prints the last \(l\) lines of a file:

tail -15 runSim.R

  return (TRUE)
}

## estimate mean only using observation with prime indices
estMeanPrimes = function (x) {
  n = length(x)
  ind = sapply(1:n, isPrime)
  return (mean(x[ind]))
}

# simulate data
x = rnorm(n)

# estimate mean
estMeanPrimes(x)

• Questions:
  • How to see the 11th line of the file and nothing else?
    
  • What about the 11th to the last line?

6.2 Piping and redirection

• | sends output from one command as input of another command.

ls -l | head -5

total 4872
-rw-r--r--  1 huazhou  staff  110345 Mar 10  2023 Emacs_Reference_Card.pdf
-rw-r--r--  1 huazhou  staff  157353 Mar 10  2023 IDRE_Winter_2019_Workshops.pdf
-rw-r--r--  1 huazhou  staff  141962 Mar 10  2023 Richard_Stallman_2013.png
-rw-r--r--  1 huazhou  staff  199492 Mar 10  2023 Vi_Cheat_Sheet.pdf

• > directs output from one command to a file.

• >> appends output from one command to a file.

• < reads input from a file.

• Combinations of shell commands (grep, sed, awk, …), piping and redirection, and regular expressions allow us pre-process and reformat huge text files efficiently.

• See HW1.

6.3 less is more; more is less

• more browses a text file screen by screen (only downwards). Scroll down one page (paging) by pressing the spacebar; exit by pressing the q key.

• less is also a pager, but has more functionalities, e.g., scroll upwards and downwards through the input.

• less doesn’t need to read the whole file, i.e., it loads files faster than more.

6.4 grep

grep prints lines that match an expression:

• Show lines that contain string CentOS:

# quotes not necessary if not a regular expression
grep 'CentOS' linux.qmd

- RHEL/CentOS is popular on servers. (In December 2020, Red Hat terminated the development of CentOS Linux distribution.)
- UCLA Hoffman2 cluster runs CentOS 7.9.2009 (as of 2023-01-01).
- Show lines that contain string `CentOS`:
grep 'CentOS' linux.qmd
grep 'CentOS' *.qmd
grep -n 'CentOS' linux.qmd
- Replace `CentOS` by `RHEL` in a text file:
sed 's/CentOS/RHEL/' linux.qmd | grep RHEL

• Search multiple text files:

grep 'CentOS' *.qmd

- RHEL/CentOS is popular on servers. (In December 2020, Red Hat terminated the development of CentOS Linux distribution.)
- UCLA Hoffman2 cluster runs CentOS 7.9.2009 (as of 2023-01-01).
- Show lines that contain string `CentOS`:
grep 'CentOS' linux.qmd
grep 'CentOS' *.qmd
grep -n 'CentOS' linux.qmd
- Replace `CentOS` by `RHEL` in a text file:
sed 's/CentOS/RHEL/' linux.qmd | grep RHEL

• Show matching line numbers:

grep -n 'CentOS' linux.qmd

51:- RHEL/CentOS is popular on servers. (In December 2020, Red Hat terminated the development of CentOS Linux distribution.)
57:- UCLA Hoffman2 cluster runs CentOS 7.9.2009 (as of 2023-01-01).
353:- Show lines that contain string `CentOS`:
356:grep 'CentOS' linux.qmd
361:grep 'CentOS' *.qmd
366:grep -n 'CentOS' linux.qmd
383:- Replace `CentOS` by `RHEL` in a text file:
385:sed 's/CentOS/RHEL/' linux.qmd | grep RHEL

• Find all files in current directory with .png extension:

ls | grep '.png$'

Richard_Stallman_2013.png
key_authentication_1.png
key_authentication_2.png
linux_directory_structure.png
linux_filepermission.png
linux_filepermission_oct.png
redhat_kills_centos.png
screenshot_top.png

• Find all directories in the current directory:

ls -al | grep '^d'

drwxr-xr-x  19 huazhou  staff     608 Dec 27 11:14 .
drwxr-xr-x  23 huazhou  staff     736 Mar 10  2023 ..

6.5 sed

• sed is a stream editor.

• Replace CentOS by RHEL in a text file:

sed 's/CentOS/RHEL/' linux.qmd | grep RHEL

- RHEL/RHEL is popular on servers. (In December 2020, Red Hat terminated the development of CentOS Linux distribution.)
- UCLA Hoffman2 cluster runs RHEL 7.9.2009 (as of 2023-01-01).
- Show lines that contain string `RHEL`:
grep 'RHEL' linux.qmd
grep 'RHEL' *.qmd
grep -n 'RHEL' linux.qmd
- Replace `RHEL` by `RHEL` in a text file:
sed 's/RHEL/RHEL/' linux.qmd | grep RHEL

6.6 awk

• awk is a filter and report writer.

• First let’s display the content of the file /etc/passwd:

cat /etc/passwd

##
# User Database
# 
# Note that this file is consulted directly only when the system is running
# in single-user mode.  At other times this information is provided by
# Open Directory.
#
# See the opendirectoryd(8) man page for additional information about
# Open Directory.
##
nobody:*:-2:-2:Unprivileged User:/var/empty:/usr/bin/false
root:*:0:0:System Administrator:/var/root:/bin/sh
daemon:*:1:1:System Services:/var/root:/usr/bin/false
_uucp:*:4:4:Unix to Unix Copy Protocol:/var/spool/uucp:/usr/sbin/uucico
_taskgated:*:13:13:Task Gate Daemon:/var/empty:/usr/bin/false
_networkd:*:24:24:Network Services:/var/networkd:/usr/bin/false
_installassistant:*:25:25:Install Assistant:/var/empty:/usr/bin/false
_lp:*:26:26:Printing Services:/var/spool/cups:/usr/bin/false
_postfix:*:27:27:Postfix Mail Server:/var/spool/postfix:/usr/bin/false
_scsd:*:31:31:Service Configuration Service:/var/empty:/usr/bin/false
_ces:*:32:32:Certificate Enrollment Service:/var/empty:/usr/bin/false
_appstore:*:33:33:Mac App Store Service:/var/db/appstore:/usr/bin/false
_mcxalr:*:54:54:MCX AppLaunch:/var/empty:/usr/bin/false
_appleevents:*:55:55:AppleEvents Daemon:/var/empty:/usr/bin/false
_geod:*:56:56:Geo Services Daemon:/var/db/geod:/usr/bin/false
_devdocs:*:59:59:Developer Documentation:/var/empty:/usr/bin/false
_sandbox:*:60:60:Seatbelt:/var/empty:/usr/bin/false
_mdnsresponder:*:65:65:mDNSResponder:/var/empty:/usr/bin/false
_ard:*:67:67:Apple Remote Desktop:/var/empty:/usr/bin/false
_www:*:70:70:World Wide Web Server:/Library/WebServer:/usr/bin/false
_eppc:*:71:71:Apple Events User:/var/empty:/usr/bin/false
_cvs:*:72:72:CVS Server:/var/empty:/usr/bin/false
_svn:*:73:73:SVN Server:/var/empty:/usr/bin/false
_mysql:*:74:74:MySQL Server:/var/empty:/usr/bin/false
_sshd:*:75:75:sshd Privilege separation:/var/empty:/usr/bin/false
_qtss:*:76:76:QuickTime Streaming Server:/var/empty:/usr/bin/false
_cyrus:*:77:6:Cyrus Administrator:/var/imap:/usr/bin/false
_mailman:*:78:78:Mailman List Server:/var/empty:/usr/bin/false
_appserver:*:79:79:Application Server:/var/empty:/usr/bin/false
_clamav:*:82:82:ClamAV Daemon:/var/virusmails:/usr/bin/false
_amavisd:*:83:83:AMaViS Daemon:/var/virusmails:/usr/bin/false
_jabber:*:84:84:Jabber XMPP Server:/var/empty:/usr/bin/false
_appowner:*:87:87:Application Owner:/var/empty:/usr/bin/false
_windowserver:*:88:88:WindowServer:/var/empty:/usr/bin/false
_spotlight:*:89:89:Spotlight:/var/empty:/usr/bin/false
_tokend:*:91:91:Token Daemon:/var/empty:/usr/bin/false
_securityagent:*:92:92:SecurityAgent:/var/db/securityagent:/usr/bin/false
_calendar:*:93:93:Calendar:/var/empty:/usr/bin/false
_teamsserver:*:94:94:TeamsServer:/var/teamsserver:/usr/bin/false
_update_sharing:*:95:-2:Update Sharing:/var/empty:/usr/bin/false
_installer:*:96:-2:Installer:/var/empty:/usr/bin/false
_atsserver:*:97:97:ATS Server:/var/empty:/usr/bin/false
_ftp:*:98:-2:FTP Daemon:/var/empty:/usr/bin/false
_unknown:*:99:99:Unknown User:/var/empty:/usr/bin/false
_softwareupdate:*:200:200:Software Update Service:/var/db/softwareupdate:/usr/bin/false
_coreaudiod:*:202:202:Core Audio Daemon:/var/empty:/usr/bin/false
_screensaver:*:203:203:Screensaver:/var/empty:/usr/bin/false
_locationd:*:205:205:Location Daemon:/var/db/locationd:/usr/bin/false
_trustevaluationagent:*:208:208:Trust Evaluation Agent:/var/empty:/usr/bin/false
_timezone:*:210:210:AutoTimeZoneDaemon:/var/empty:/usr/bin/false
_lda:*:211:211:Local Delivery Agent:/var/empty:/usr/bin/false
_cvmsroot:*:212:212:CVMS Root:/var/empty:/usr/bin/false
_usbmuxd:*:213:213:iPhone OS Device Helper:/var/db/lockdown:/usr/bin/false
_dovecot:*:214:6:Dovecot Administrator:/var/empty:/usr/bin/false
_dpaudio:*:215:215:DP Audio:/var/empty:/usr/bin/false
_postgres:*:216:216:PostgreSQL Server:/var/empty:/usr/bin/false
_krbtgt:*:217:-2:Kerberos Ticket Granting Ticket:/var/empty:/usr/bin/false
_kadmin_admin:*:218:-2:Kerberos Admin Service:/var/empty:/usr/bin/false
_kadmin_changepw:*:219:-2:Kerberos Change Password Service:/var/empty:/usr/bin/false
_devicemgr:*:220:220:Device Management Server:/var/empty:/usr/bin/false
_webauthserver:*:221:221:Web Auth Server:/var/empty:/usr/bin/false
_netbios:*:222:222:NetBIOS:/var/empty:/usr/bin/false
_warmd:*:224:224:Warm Daemon:/var/empty:/usr/bin/false
_dovenull:*:227:227:Dovecot Authentication:/var/empty:/usr/bin/false
_netstatistics:*:228:228:Network Statistics Daemon:/var/empty:/usr/bin/false
_avbdeviced:*:229:-2:Ethernet AVB Device Daemon:/var/empty:/usr/bin/false
_krb_krbtgt:*:230:-2:Open Directory Kerberos Ticket Granting Ticket:/var/empty:/usr/bin/false
_krb_kadmin:*:231:-2:Open Directory Kerberos Admin Service:/var/empty:/usr/bin/false
_krb_changepw:*:232:-2:Open Directory Kerberos Change Password Service:/var/empty:/usr/bin/false
_krb_kerberos:*:233:-2:Open Directory Kerberos:/var/empty:/usr/bin/false
_krb_anonymous:*:234:-2:Open Directory Kerberos Anonymous:/var/empty:/usr/bin/false
_assetcache:*:235:235:Asset Cache Service:/var/empty:/usr/bin/false
_coremediaiod:*:236:236:Core Media IO Daemon:/var/empty:/usr/bin/false
_launchservicesd:*:239:239:_launchservicesd:/var/empty:/usr/bin/false
_iconservices:*:240:240:IconServices:/var/empty:/usr/bin/false
_distnote:*:241:241:DistNote:/var/empty:/usr/bin/false
_nsurlsessiond:*:242:242:NSURLSession Daemon:/var/db/nsurlsessiond:/usr/bin/false
_displaypolicyd:*:244:244:Display Policy Daemon:/var/empty:/usr/bin/false
_astris:*:245:245:Astris Services:/var/db/astris:/usr/bin/false
_krbfast:*:246:-2:Kerberos FAST Account:/var/empty:/usr/bin/false
_gamecontrollerd:*:247:247:Game Controller Daemon:/var/empty:/usr/bin/false
_mbsetupuser:*:248:248:Setup User:/var/setup:/bin/bash
_ondemand:*:249:249:On Demand Resource Daemon:/var/db/ondemand:/usr/bin/false
_xserverdocs:*:251:251:macOS Server Documents Service:/var/empty:/usr/bin/false
_wwwproxy:*:252:252:WWW Proxy:/var/empty:/usr/bin/false
_mobileasset:*:253:253:MobileAsset User:/var/ma:/usr/bin/false
_findmydevice:*:254:254:Find My Device Daemon:/var/db/findmydevice:/usr/bin/false
_datadetectors:*:257:257:DataDetectors:/var/db/datadetectors:/usr/bin/false
_captiveagent:*:258:258:captiveagent:/var/empty:/usr/bin/false
_ctkd:*:259:259:ctkd Account:/var/empty:/usr/bin/false
_applepay:*:260:260:applepay Account:/var/db/applepay:/usr/bin/false
_hidd:*:261:261:HID Service User:/var/db/hidd:/usr/bin/false
_cmiodalassistants:*:262:262:CoreMedia IO Assistants User:/var/db/cmiodalassistants:/usr/bin/false
_analyticsd:*:263:263:Analytics Daemon:/var/db/analyticsd:/usr/bin/false
_fpsd:*:265:265:FPS Daemon:/var/db/fpsd:/usr/bin/false
_timed:*:266:266:Time Sync Daemon:/var/db/timed:/usr/bin/false
_nearbyd:*:268:268:Proximity and Ranging Daemon:/var/db/nearbyd:/usr/bin/false
_reportmemoryexception:*:269:269:ReportMemoryException:/var/db/reportmemoryexception:/usr/bin/false
_driverkit:*:270:270:DriverKit:/var/empty:/usr/bin/false
_diskimagesiod:*:271:271:DiskImages IO Daemon:/var/db/diskimagesiod:/usr/bin/false
_logd:*:272:272:Log Daemon:/var/db/diagnostics:/usr/bin/false
_appinstalld:*:273:273:App Install Daemon:/var/db/appinstalld:/usr/bin/false
_installcoordinationd:*:274:274:Install Coordination Daemon:/var/db/installcoordinationd:/usr/bin/false
_demod:*:275:275:Demo Daemon:/var/empty:/usr/bin/false
_rmd:*:277:277:Remote Management Daemon:/var/db/rmd:/usr/bin/false
_accessoryupdater:*:278:278:Accessory Update Daemon:/var/db/accessoryupdater:/usr/bin/false
_knowledgegraphd:*:279:279:Knowledge Graph Daemon:/var/db/knowledgegraphd:/usr/bin/false
_coreml:*:280:280:CoreML Services:/var/db/coreml:/usr/bin/false
_sntpd:*:281:281:SNTP Server Daemon:/var/empty:/usr/bin/false
_trustd:*:282:282:trustd:/var/empty:/usr/bin/false
_mmaintenanced:*:283:283:mmaintenanced:/var/db/mmaintenanced:/usr/bin/false
_darwindaemon:*:284:284:Darwin Daemon:/var/db/darwindaemon:/usr/bin/false
_notification_proxy:*:285:285:Notification Proxy:/var/empty:/usr/bin/false
_avphidbridge:*:288:288:Apple Virtual Platform HID Bridge:/var/empty:/usr/bin/false
_biome:*:289:289:Biome:/var/db/biome:/usr/bin/false
_backgroundassets:*:291:291:Background Assets Service:/var/empty:/usr/bin/false
_mobilegestalthelper:*:293:293:MobileGestaltHelper:/var/empty:/usr/bin/false
_audiomxd:*:294:294:Audio and MediaExperience Daemon:/var/db/audiomxd:/usr/bin/false
_terminusd:*:295:295:Terminus:/var/empty:/usr/bin/false
_neuralengine:*:296:296:AppleNeuralEngine:/var/db/neuralengine:/usr/bin/false
_oahd:*:441:441:OAH Daemon:/var/empty:/usr/bin/false

Each line contains fields (1) user name, (2) password, (3) user ID, (4) group ID, (5) user ID info, (6) home directory, and (7) command shell, separated by :.

• Print sorted list of login names:

awk -F: '{ print $1 }' /etc/passwd | sort | head -10

#
# 
# Note that this file is consulted directly only when the system is running
# Open Directory.
# Open Directory.
# See the opendirectoryd(8) man page for additional information about
# User Database
# in single-user mode.  At other times this information is provided by
##
##

• Print number of lines in a file, as NR stands for Number of Rows:

awk 'END { print NR }' /etc/passwd

131

or

wc -l /etc/passwd

     131 /etc/passwd

or (not displaying file name)

wc -l < /etc/passwd

     131

• Print login names with UID in range 1000-1035:

awk -F: '{if ($3 >= 1000 && $3 <= 1047) print}' /etc/passwd

• Print login names and log-in shells in comma-separated format:

awk -F: '{OFS = ","} {print $1, $7}' /etc/passwd

##,
# User Database,
# ,
# Note that this file is consulted directly only when the system is running,
# in single-user mode.  At other times this information is provided by,
# Open Directory.,
#,
# See the opendirectoryd(8) man page for additional information about,
# Open Directory.,
##,
nobody,/usr/bin/false
root,/bin/sh
daemon,/usr/bin/false
_uucp,/usr/sbin/uucico
_taskgated,/usr/bin/false
_networkd,/usr/bin/false
_installassistant,/usr/bin/false
_lp,/usr/bin/false
_postfix,/usr/bin/false
_scsd,/usr/bin/false
_ces,/usr/bin/false
_appstore,/usr/bin/false
_mcxalr,/usr/bin/false
_appleevents,/usr/bin/false
_geod,/usr/bin/false
_devdocs,/usr/bin/false
_sandbox,/usr/bin/false
_mdnsresponder,/usr/bin/false
_ard,/usr/bin/false
_www,/usr/bin/false
_eppc,/usr/bin/false
_cvs,/usr/bin/false
_svn,/usr/bin/false
_mysql,/usr/bin/false
_sshd,/usr/bin/false
_qtss,/usr/bin/false
_cyrus,/usr/bin/false
_mailman,/usr/bin/false
_appserver,/usr/bin/false
_clamav,/usr/bin/false
_amavisd,/usr/bin/false
_jabber,/usr/bin/false
_appowner,/usr/bin/false
_windowserver,/usr/bin/false
_spotlight,/usr/bin/false
_tokend,/usr/bin/false
_securityagent,/usr/bin/false
_calendar,/usr/bin/false
_teamsserver,/usr/bin/false
_update_sharing,/usr/bin/false
_installer,/usr/bin/false
_atsserver,/usr/bin/false
_ftp,/usr/bin/false
_unknown,/usr/bin/false
_softwareupdate,/usr/bin/false
_coreaudiod,/usr/bin/false
_screensaver,/usr/bin/false
_locationd,/usr/bin/false
_trustevaluationagent,/usr/bin/false
_timezone,/usr/bin/false
_lda,/usr/bin/false
_cvmsroot,/usr/bin/false
_usbmuxd,/usr/bin/false
_dovecot,/usr/bin/false
_dpaudio,/usr/bin/false
_postgres,/usr/bin/false
_krbtgt,/usr/bin/false
_kadmin_admin,/usr/bin/false
_kadmin_changepw,/usr/bin/false
_devicemgr,/usr/bin/false
_webauthserver,/usr/bin/false
_netbios,/usr/bin/false
_warmd,/usr/bin/false
_dovenull,/usr/bin/false
_netstatistics,/usr/bin/false
_avbdeviced,/usr/bin/false
_krb_krbtgt,/usr/bin/false
_krb_kadmin,/usr/bin/false
_krb_changepw,/usr/bin/false
_krb_kerberos,/usr/bin/false
_krb_anonymous,/usr/bin/false
_assetcache,/usr/bin/false
_coremediaiod,/usr/bin/false
_launchservicesd,/usr/bin/false
_iconservices,/usr/bin/false
_distnote,/usr/bin/false
_nsurlsessiond,/usr/bin/false
_displaypolicyd,/usr/bin/false
_astris,/usr/bin/false
_krbfast,/usr/bin/false
_gamecontrollerd,/usr/bin/false
_mbsetupuser,/bin/bash
_ondemand,/usr/bin/false
_xserverdocs,/usr/bin/false
_wwwproxy,/usr/bin/false
_mobileasset,/usr/bin/false
_findmydevice,/usr/bin/false
_datadetectors,/usr/bin/false
_captiveagent,/usr/bin/false
_ctkd,/usr/bin/false
_applepay,/usr/bin/false
_hidd,/usr/bin/false
_cmiodalassistants,/usr/bin/false
_analyticsd,/usr/bin/false
_fpsd,/usr/bin/false
_timed,/usr/bin/false
_nearbyd,/usr/bin/false
_reportmemoryexception,/usr/bin/false
_driverkit,/usr/bin/false
_diskimagesiod,/usr/bin/false
_logd,/usr/bin/false
_appinstalld,/usr/bin/false
_installcoordinationd,/usr/bin/false
_demod,/usr/bin/false
_rmd,/usr/bin/false
_accessoryupdater,/usr/bin/false
_knowledgegraphd,/usr/bin/false
_coreml,/usr/bin/false
_sntpd,/usr/bin/false
_trustd,/usr/bin/false
_mmaintenanced,/usr/bin/false
_darwindaemon,/usr/bin/false
_notification_proxy,/usr/bin/false
_avphidbridge,/usr/bin/false
_biome,/usr/bin/false
_backgroundassets,/usr/bin/false
_mobilegestalthelper,/usr/bin/false
_audiomxd,/usr/bin/false
_terminusd,/usr/bin/false
_neuralengine,/usr/bin/false
_oahd,/usr/bin/false

• Print login names and indicate those with UID>1000 as vip:

awk -F: -v status="" '{OFS = ","} 
{if ($3 >= 1000) status="vip"; else status="regular"} 
{print $1, status}' /etc/passwd

##,regular
# User Database,regular
# ,regular
# Note that this file is consulted directly only when the system is running,regular
# in single-user mode.  At other times this information is provided by,regular
# Open Directory.,regular
#,regular
# See the opendirectoryd(8) man page for additional information about,regular
# Open Directory.,regular
##,regular
nobody,regular
root,regular
daemon,regular
_uucp,regular
_taskgated,regular
_networkd,regular
_installassistant,regular
_lp,regular
_postfix,regular
_scsd,regular
_ces,regular
_appstore,regular
_mcxalr,regular
_appleevents,regular
_geod,regular
_devdocs,regular
_sandbox,regular
_mdnsresponder,regular
_ard,regular
_www,regular
_eppc,regular
_cvs,regular
_svn,regular
_mysql,regular
_sshd,regular
_qtss,regular
_cyrus,regular
_mailman,regular
_appserver,regular
_clamav,regular
_amavisd,regular
_jabber,regular
_appowner,regular
_windowserver,regular
_spotlight,regular
_tokend,regular
_securityagent,regular
_calendar,regular
_teamsserver,regular
_update_sharing,regular
_installer,regular
_atsserver,regular
_ftp,regular
_unknown,regular
_softwareupdate,regular
_coreaudiod,regular
_screensaver,regular
_locationd,regular
_trustevaluationagent,regular
_timezone,regular
_lda,regular
_cvmsroot,regular
_usbmuxd,regular
_dovecot,regular
_dpaudio,regular
_postgres,regular
_krbtgt,regular
_kadmin_admin,regular
_kadmin_changepw,regular
_devicemgr,regular
_webauthserver,regular
_netbios,regular
_warmd,regular
_dovenull,regular
_netstatistics,regular
_avbdeviced,regular
_krb_krbtgt,regular
_krb_kadmin,regular
_krb_changepw,regular
_krb_kerberos,regular
_krb_anonymous,regular
_assetcache,regular
_coremediaiod,regular
_launchservicesd,regular
_iconservices,regular
_distnote,regular
_nsurlsessiond,regular
_displaypolicyd,regular
_astris,regular
_krbfast,regular
_gamecontrollerd,regular
_mbsetupuser,regular
_ondemand,regular
_xserverdocs,regular
_wwwproxy,regular
_mobileasset,regular
_findmydevice,regular
_datadetectors,regular
_captiveagent,regular
_ctkd,regular
_applepay,regular
_hidd,regular
_cmiodalassistants,regular
_analyticsd,regular
_fpsd,regular
_timed,regular
_nearbyd,regular
_reportmemoryexception,regular
_driverkit,regular
_diskimagesiod,regular
_logd,regular
_appinstalld,regular
_installcoordinationd,regular
_demod,regular
_rmd,regular
_accessoryupdater,regular
_knowledgegraphd,regular
_coreml,regular
_sntpd,regular
_trustd,regular
_mmaintenanced,regular
_darwindaemon,regular
_notification_proxy,regular
_avphidbridge,regular
_biome,regular
_backgroundassets,regular
_mobilegestalthelper,regular
_audiomxd,regular
_terminusd,regular
_neuralengine,regular
_oahd,regular

6.7 Text editors

Source: Editor War on Wikipedia.

6.7.1 Emacs

• Emacs is a powerful text editor with extensive support for many languages including R, \(\LaTeX\), python, and C/C++; however it’s not installed by default on many Linux distributions.

• Basic survival commands:

  • emacs filename to open a file with emacs.
    
  • CTRL-x CTRL-f to open an existing or new file.
    
  • CTRL-x CTRX-s to save.
    
  • CTRL-x CTRL-w to save as.
    
  • CTRL-x CTRL-c to quit.

• Google emacs cheatsheet

C-<key> means hold the control key, and press <key>.
M-<key> means press the Esc key once, and press <key>.

6.7.2 Vi

• Vi is ubiquitous (POSIX standard). Learn at least its basics; otherwise you can edit nothing on some clusters.

• Basic survival commands:

  • vi filename to start editing a file.
  • vi is a modal editor: insert mode and normal mode. Pressing i switches from the normal mode to insert mode. Pressing ESC switches from the insert mode to normal mode.
    
  • :x<Return> quits vi and saves changes.
    
  • :q!<Return> quits vi without saving latest changes.
    
  • :w<Return> saves changes.
  • :wq<Return> quits vi and saves changes.

• Google vi cheatsheet

7 IDE (Integrated Development Environment)

• Statisticians/data scientists write a lot of code. Critical to adopt a good IDE that goes beyond code editing: syntax highlighting, executing code within editor, debugging, profiling, version control, etc.

• RStudio, Eclipse, Emacs, Matlab, Visual Studio, VS Code, etc.

8 Processes

8.1 Cancel a non-responding program

• Press Ctrl+C to cancel a non-responding or long-running program.

8.2 Processes

• OS runs processes on behalf of user.

• Each process has Process ID (PID), Username (UID), Parent process ID (PPID), Time and data process started (STIME), time running (TIME), etc.

ps

  PID TTY           TIME CMD
38079 ttys000    0:00.04 -zsh

• All current running processes:

ps -eaf

  UID   PID  PPID   C STIME   TTY           TIME CMD
    0     1     0   0 Sat10AM ??        51:33.10 /sbin/launchd
    0   500     1   0 Sat11AM ??         7:53.76 /usr/libexec/logd
    0   501     1   0 Sat11AM ??         0:00.36 /usr/libexec/smd
    0   502     1   0 Sat11AM ??         1:29.71 /usr/libexec/UserEventAgent (System)
    0   504     1   0 Sat11AM ??         0:06.09 /System/Library/PrivateFrameworks/Uninstall.framework/Resources/uninstalld
    0   505     1   0 Sat11AM ??         6:12.34 /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/FSEvents.framework/Versions/A/Support/fseventsd
    0   506     1   0 Sat11AM ??         0:09.96 /System/Library/PrivateFrameworks/MediaRemote.framework/Support/mediaremoted
    0   509     1   0 Sat11AM ??         0:16.93 /usr/sbin/systemstats --daemon
  278   511     1   0 Sat11AM ??         0:00.43 /System/Library/PrivateFrameworks/MobileAccessoryUpdater.framework/Support/accessoryupdaterd 120
    0   512     1   0 Sat11AM ??         2:01.67 /usr/libexec/configd
    0   513     1   0 Sat11AM ??         0:00.03 endpointsecurityd
    0   514     1   0 Sat11AM ??         1:45.82 /System/Library/CoreServices/powerd.bundle/powerd
    0   515     1   0 Sat11AM ??         0:00.67 /usr/libexec/IOMFB_bics_daemon
  289   516     1   0 Sat11AM ??         0:10.02 /System/Library/PrivateFrameworks/BiomeStreams.framework/Support/biomed
    0   518     1   0 Sat11AM ??         0:03.93 /usr/libexec/amfid
    0   520     1   0 Sat11AM ??         0:05.91 /usr/libexec/remoted
    0   522     1   0 Sat11AM ??         0:00.06 /usr/libexec/keybagd -t 15
  200   523     1   0 Sat11AM ??         0:00.81 /System/Library/PrivateFrameworks/MobileSoftwareUpdate.framework/Support/softwareupdated
    0   525     1   0 Sat11AM ??         0:02.92 /usr/libexec/watchdogd
  240   530     1   0 Sat11AM ??         0:00.42 /System/Library/CoreServices/iconservicesd
    0   531     1   0 Sat11AM ??         0:00.72 /usr/libexec/kernelmanagerd
    0   532     1   0 Sat11AM ??         2:31.34 /usr/libexec/diskarbitrationd
    0   536     1   0 Sat11AM ??         4:00.50 /usr/libexec/coreduetd
    0   537     1   0 Sat11AM ??         0:09.65 /usr/sbin/syslogd
    0   540     1   0 Sat11AM ??         0:28.70 /usr/libexec/thermalmonitord
    0   541     1   0 Sat11AM ??         5:52.72 /usr/libexec/opendirectoryd
    0   542     1   0 Sat11AM ??         1:17.37 /System/Library/PrivateFrameworks/ApplePushService.framework/apsd
    0   543     1   0 Sat11AM ??         1:03.82 /System/Library/CoreServices/launchservicesd
  266   544     1   0 Sat11AM ??         0:03.03 /usr/libexec/timed
  213   545     1   0 Sat11AM ??         0:40.25 /System/Library/PrivateFrameworks/MobileDevice.framework/Versions/A/Resources/usbmuxd -launchd
    0   546     1   0 Sat11AM ??         0:26.83 /usr/sbin/securityd -i
    0   547     1   0 Sat11AM ??         0:00.01 auditd -l
  205   549     1   0 Sat11AM ??         6:06.31 /usr/libexec/locationd
    0   551     1   0 Sat11AM ??         0:00.01 autofsd
    0   552     1   0 Sat11AM ??         4:01.37 /usr/libexec/dasd
  241   554     1   0 Sat11AM ??        20:00.52 /usr/sbin/distnoted daemon
    0   555     1   0 Sat11AM ??         0:00.09 /System/Library/PrivateFrameworks/AppleCredentialManager.framework/AppleCredentialManagerDaemon
    0   557     1   0 Sat11AM ??         0:00.02 /usr/libexec/dirhelper
    0   558     1   0 Sat11AM ??         0:00.07 /System/Library/CoreServices/logind
    0   559     1   0 Sat11AM ??         0:00.65 /System/Library/PrivateFrameworks/GenerationalStorage.framework/Versions/A/Support/revisiond
    0   560     1   0 Sat11AM ??         0:00.01 /usr/sbin/KernelEventAgent
    0   561     1   0 Sat11AM ??         0:01.87 /usr/libexec/usermanagerd -t 15
    0   563     1   0 Sat11AM ??         6:00.42 /usr/sbin/bluetoothd
    0   564     1   0 Sat11AM ??         2:55.91 /usr/sbin/notifyd
    0   565     1   0 Sat11AM ??         5:03.67 /usr/libexec/sandboxd
    0   566     1   0 Sat11AM ??         2:18.92 /usr/libexec/corebrightnessd --launchd
    0   567     1   0 Sat11AM ??         0:11.72 /usr/libexec/AirPlayXPCHelper
    0   568     1   0 Sat11AM ??         0:03.17 /System/Library/Frameworks/CoreMediaIO.framework/Versions/A/Resources/com.apple.cmio.registerassistantservice
    0   569     1   0 Sat11AM ??         0:03.75 /usr/libexec/logd_helper
   88   570     1   0 Sat11AM ??       229:26.53 /System/Library/PrivateFrameworks/SkyLight.framework/Resources/WindowServer -daemon
    0   571     1   0 Sat11AM ??         2:46.36 /usr/sbin/cfprefsd daemon
    0   572     1   0 Sat11AM ??         0:57.52 /System/Library/PrivateFrameworks/TCC.framework/Support/tccd system
    0   574     1   0 Sat11AM ??         1:03.83 /usr/libexec/lsd runAsRoot
    0   575     1   0 Sat11AM ??         0:00.12 aslmanager
    0   576     1   0 Sat11AM ??         0:37.23 /System/Library/PrivateFrameworks/CoreDuetContext.framework/Resources/contextstored
    0   577     1   0 Sat11AM ??         0:12.01 /System/Library/CoreServices/coreservicesd
    0   578     1   0 Sat11AM ??         5:58.23 /usr/libexec/runningboardd
  202   582     1   0 Sat11AM ??        18:21.78 /usr/sbin/coreaudiod
  282   589     1   0 Sat11AM ??         6:15.96 /usr/libexec/trustd
    0   590     1   0 Sat11AM ??         1:22.00 /usr/libexec/apfsd
    0   591     1   0 Sat11AM ??         0:04.65 /usr/libexec/nehelper
  242   592     1   0 Sat11AM ??         0:09.28 /usr/libexec/nsurlsessiond --privileged
    0   593     1   0 Sat11AM ??        14:45.08 /usr/libexec/airportd
    0   594     1   0 Sat11AM ??         0:00.13 /System/Library/PrivateFrameworks/CoreAccessories.framework/Support/accessoryd
    0   595     1   0 Sat11AM ??         0:00.21 /usr/libexec/usbd
  263   596     1   0 Sat11AM ??         0:33.40 /System/Library/PrivateFrameworks/CoreAnalytics.framework/Support/analyticsd
    0   597     1   0 Sat11AM ??         0:00.95 /usr/libexec/biometrickitd --launchd
    0   599     1   0 Sat11AM ??         0:00.04 /usr/libexec/trustdFileHelper
    0   602     1   0 Sat11AM ??         0:00.30 /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/XPCServices/csnameddatad.xpc/Contents/MacOS/csnameddatad
    0   603     1   0 Sat11AM ??         1:41.48 /usr/sbin/distnoted agent
    0   605     1   0 Sat11AM ??         0:24.31 /System/Library/CoreServices/backupd.bundle/Contents/Resources/backupd-helper -launchd
    0   607     1   0 Sat11AM ??         0:01.04 /usr/libexec/PowerUIAgent
    0   608     1   0 Sat11AM ??         0:00.01 /usr/libexec/cryptexd
  202   610     1   0 Sat11AM ??         1:09.43 /usr/sbin/distnoted agent
    0   612     1   0 Sat11AM ??         5:44.69 /usr/libexec/mobileassetd
   65   619     1   0 Sat11AM ??         1:57.04 /usr/sbin/mDNSResponder
    0   630     1   0 Sat11AM ??         0:04.00 /System/Library/PrivateFrameworks/SystemStatusServer.framework/Support/systemstatusd
  261   638     1   0 Sat11AM ??         0:00.05 /usr/libexec/hidd
   88   641     1   0 Sat11AM ??         1:10.74 /usr/sbin/distnoted agent
    0   659     1   0 Sat11AM ??         2:28.45 /System/Library/Frameworks/Security.framework/Versions/A/XPCServices/authd.xpc/Contents/MacOS/authd
    0   663     1   0 Sat11AM ??         0:00.74 /usr/libexec/secinitd
    0   664     1   0 Sat11AM ??         0:01.00 /usr/libexec/securityd_system
    0   667     1   0 Sat11AM ??        11:27.70 /usr/libexec/storagekitd
  202   669     1   0 Sat11AM ??         0:08.51 Core Audio Driver (MSTeamsAudioDevice.driver)
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    0   681     1   0 Sat11AM ??         0:00.01 /System/Library/Frameworks/ColorSync.framework/Versions/A/XPCServices/com.apple.ColorSyncXPCAgent.xpc/Contents/MacOS/com.apple.ColorSyncXPCAgent
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  278   788     1   0 Sat11AM ??         0:00.04 /System/Library/PrivateFrameworks/MobileAccessoryUpdater.framework/XPCServices/UARPUpdaterServiceAFU.xpc/Contents/MacOS/UARPUpdaterServiceAFU
  278   789     1   0 Sat11AM ??         0:00.15 /System/Library/PrivateFrameworks/MobileAccessoryUpdater.framework/XPCServices/UARPUpdaterServiceLegacyAudio.xpc/Contents/MacOS/UARPUpdaterServiceLegacyAudio
  278   790     1   0 Sat11AM ??         0:05.06 /System/Library/PrivateFrameworks/MobileAccessoryUpdater.framework/XPCServices/UARPUpdaterServiceUSBPD.xpc/Contents/MacOS/UARPUpdaterServiceUSBPD
  278   791     1   0 Sat11AM ??         0:00.07 /System/Library/PrivateFrameworks/MobileAccessoryUpdater.framework/XPCServices/UARPUpdaterServiceHID.xpc/Contents/MacOS/UARPUpdaterServiceHID
  278   792     1   0 Sat11AM ??         0:00.07 /System/Library/PrivateFrameworks/MobileAccessoryUpdater.framework/XPCServices/ThunderboltAccessoryUpdaterService.xpc/Contents/MacOS/ThunderboltAccessoryUpdaterService
  278   793     1   0 Sat11AM ??         0:06.23 /System/Library/PrivateFrameworks/GeoServices.framework/Versions/A/XPCServices/com.apple.geod.xpc/Contents/MacOS/com.apple.geod
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   89  1329     1   0 Sat11AM ??         0:17.04 /System/Library/Frameworks/CoreServices.framework/Frameworks/Metadata.framework/Versions/A/Support/mdbulkimport -s mdworker-bundle -c MDSImporterBundleFinder -m com.apple.metadata.mdbulkimport
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  504 27675 27511   0  9:51AM ??         0:00.13 /Applications/Utilities/Adobe Creative Cloud/ACC/Creative Cloud.app/Contents/MacOS/../Frameworks/Creative Cloud UI Helper.app/Contents/MacOS/Creative Cloud UI Helper --type=utility --utility-sub-type=network.mojom.NetworkService --lang=en --service-sandbox-type=network --no-sandbox --use-mock-keychain --locales-dir-path=/Library/Application Support/Adobe/Adobe Desktop Common/CEF/Chromium Embedded Framework.framework/Resources --log-severity=warning --user-agent=Mozilla/5.0 (Macintosh; Apple Silicon14_2_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/116.0.5845.190 Safari/537.36 CreativeCloud/6.1.0.587 --lang=en --user-data-dir=/Users/huazhou/Library/Application Support/CEF/User Data --log-file=/Users/huazhou/Library/Logs/CreativeCloud/ACC/CEF.log --shared-files --field-trial-handle=1718379636,r,2999415095704817102,13308755814634682942,262144 --disable-features=BackForwardCache,DocumentPictureInPictureAPI
  504 27676 27511   0  9:51AM ??         0:19.14 /Applications/Utilities/Adobe Creative Cloud/ACC/Creative Cloud.app/Contents/MacOS/../Frameworks/Creative Cloud UI Helper (Renderer).app/Contents/MacOS/Creative Cloud UI Helper (Renderer) --type=renderer --locales-dir-path=/Library/Application Support/Adobe/Adobe Desktop Common/CEF/Chromium Embedded Framework.framework/Resources --log-severity=warning --user-agent=Mozilla/5.0 (Macintosh; Apple Silicon14_2_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/116.0.5845.190 Safari/537.36 CreativeCloud/6.1.0.587 --user-data-dir=/Users/huazhou/Library/Application Support/CEF/User Data --first-renderer-process --no-sandbox --autoplay-policy=no-user-gesture-required --log-file=/Users/huazhou/Library/Logs/CreativeCloud/ACC/CEF.log --js-flags=--expose-gc --lang=en --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=5 --time-ticks-at-unix-epoch=-1703506631826089 --launch-time-ticks=192880339521 --shared-files --field-trial-handle=1718379636,r,2999415095704817102,13308755814634682942,262144 --disable-features=BackForwardCache,DocumentPictureInPictureAPI
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  504 27688 27537   0  9:51AM ??         0:00.03 /Applications/Box.app/Contents/MacOS/python -B -c from multiprocessing.resource_tracker import main;main(31)
  504 27721     1   0  9:51AM ??         0:00.02 /System/Library/Frameworks/AudioToolbox.framework/XPCServices/com.apple.audio.SandboxHelper.xpc/Contents/MacOS/com.apple.audio.SandboxHelper
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  504 27875     1   0  9:51AM ??         0:00.06 /System/Library/PrivateFrameworks/AssetCacheServices.framework/Versions/A/XPCServices/AssetCacheLocatorService.xpc/Contents/MacOS/AssetCacheLocatorService -a
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  504 28019     1   0  9:52AM ??         0:00.02 /System/Library/Frameworks/AudioToolbox.framework/XPCServices/com.apple.audio.SandboxHelper.xpc/Contents/MacOS/com.apple.audio.SandboxHelper
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  504 33143     1   0 10:28AM ??         0:00.56 /System/Library/Frameworks/AppKit.framework/Versions/C/XPCServices/com.apple.appkit.xpc.openAndSavePanelService.xpc/Contents/MacOS/com.apple.appkit.xpc.openAndSavePanelService
  504 33147     1   0 10:28AM ??         0:00.10 /System/Library/Frameworks/QuickLookUI.framework/Versions/A/XPCServices/QuickLookUIService.xpc/Contents/MacOS/QuickLookUIService
  504 33901     1   0 10:36AM ??         0:01.45 /System/Library/Frameworks/AppKit.framework/Versions/C/XPCServices/com.apple.appkit.xpc.openAndSavePanelService.xpc/Contents/MacOS/com.apple.appkit.xpc.openAndSavePanelService
  504 33902     1   0 10:36AM ??         0:00.09 /System/Library/Frameworks/QuickLookUI.framework/Versions/A/XPCServices/QuickLookUIService.xpc/Contents/MacOS/QuickLookUIService
  504 34032     1   0 10:38AM ??         0:03.27 /System/Library/Input Methods/SCIM.app/Contents/PlugIns/SCIM_Extension.appex/Contents/MacOS/SCIM_Extension -AppleLanguages ("en-US", "zh-Hans-US")
  504 34196 27210   0 10:39AM ??         0:00.92 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper (Renderer).app/Contents/MacOS/Google Chrome Helper (Renderer) --type=renderer --origin-trial-disabled-features=WebGPU --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=155 --time-ticks-at-unix-epoch=-1703506631900517 --launch-time-ticks=195711088112 --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=230
  504 34197     1   0 10:39AM ??         0:00.05 /usr/libexec/mlruntimed
  504 34837     1   0 10:41AM ??         0:00.56 /System/Library/Frameworks/VideoToolbox.framework/Versions/A/XPCServices/VTEncoderXPCService.xpc/Contents/MacOS/VTEncoderXPCService
  504 34843     1   0 10:41AM ??         0:00.02 /System/Library/Frameworks/AudioToolbox.framework/XPCServices/com.apple.audio.SandboxHelper.xpc/Contents/MacOS/com.apple.audio.SandboxHelper
  504 34844     1   0 10:41AM ??         0:00.14 /System/Library/Frameworks/VideoToolbox.framework/Versions/A/XPCServices/VTDecoderXPCService.xpc/Contents/MacOS/VTDecoderXPCService
  504 37489 27210   0 11:01AM ??         0:01.56 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper (Renderer).app/Contents/MacOS/Google Chrome Helper (Renderer) --type=renderer --origin-trial-disabled-features=WebGPU --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=223 --time-ticks-at-unix-epoch=-1703506631900517 --launch-time-ticks=197064686007 --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=192
  504 37513     1   0 11:02AM ??         0:00.02 /System/Library/Frameworks/AudioToolbox.framework/XPCServices/com.apple.audio.SandboxHelper.xpc/Contents/MacOS/com.apple.audio.SandboxHelper
  504 37514     1   0 11:02AM ??         0:00.81 /System/Library/Frameworks/VideoToolbox.framework/Versions/A/XPCServices/VTEncoderXPCService.xpc/Contents/MacOS/VTEncoderXPCService
  504 37515     1   0 11:02AM ??         0:00.01 /System/Library/Frameworks/AudioToolbox.framework/XPCServices/com.apple.audio.SandboxHelper.xpc/Contents/MacOS/com.apple.audio.SandboxHelper
  504 37516     1   0 11:02AM ??         0:00.11 /System/Library/CoreServices/OSDUIHelper.app/Contents/MacOS/OSDUIHelper
  504 37566 27210   0 11:02AM ??         0:03.96 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper (Renderer).app/Contents/MacOS/Google Chrome Helper (Renderer) --type=renderer --origin-trial-disabled-features=WebGPU --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=225 --time-ticks-at-unix-epoch=-1703506631900517 --launch-time-ticks=197137199414 --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=192
  504 38096 27210   0 11:08AM ??         0:00.06 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper.app/Contents/MacOS/Google Chrome Helper --type=utility --utility-sub-type=data_decoder.mojom.DataDecoderService --lang=en-US --service-sandbox-type=service --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=192
  504 38103 27210   0 11:08AM ??         0:01.94 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper (Renderer).app/Contents/MacOS/Google Chrome Helper (Renderer) --type=renderer --origin-trial-disabled-features=WebGPU --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=237 --time-ticks-at-unix-epoch=-1703506631900517 --launch-time-ticks=197469685778 --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=192
  504 38108 27210   0 11:08AM ??         0:00.54 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper (Renderer).app/Contents/MacOS/Google Chrome Helper (Renderer) --type=renderer --origin-trial-disabled-features=WebGPU --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=238 --time-ticks-at-unix-epoch=-1703506631900517 --launch-time-ticks=197472588096 --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=211
  504 38127 27210   0 11:08AM ??         0:01.81 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper (Renderer).app/Contents/MacOS/Google Chrome Helper (Renderer) --type=renderer --origin-trial-disabled-features=WebGPU --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=250 --time-ticks-at-unix-epoch=-1703506631900517 --launch-time-ticks=197495431472 --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=192
  504 38166 27210   0 11:08AM ??         0:00.05 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper (Renderer).app/Contents/MacOS/Google Chrome Helper (Renderer) --type=renderer --origin-trial-disabled-features=WebGPU --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=251 --time-ticks-at-unix-epoch=-1703506631900517 --launch-time-ticks=197496407844 --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=211
  504 39077     1   0 11:10AM ??         0:00.08 /System/Library/PrivateFrameworks/AOSKit.framework/Versions/A/XPCServices/com.apple.iCloudHelper.xpc/Contents/MacOS/com.apple.iCloudHelper
  504 39500     1   0 11:11AM ??         0:00.52 /System/Library/CoreServices/UserNotificationCenter.app/Contents/MacOS/UserNotificationCenter
  504 39717     1   0 11:12AM ??         0:00.11 /System/Library/Frameworks/CoreServices.framework/Frameworks/Metadata.framework/Versions/A/Support/mdworker_shared -s mdworker -c MDSImporterWorker -m com.apple.mdworker.shared
  504 39730     1   0 11:12AM ??         0:03.67 /Applications/RStudio.app/Contents/MacOS/RStudio
  504 39731 39730   0 11:12AM ??         0:01.74 /Applications/RStudio.app/Contents/Frameworks/RStudio Helper (GPU).app/Contents/MacOS/RStudio Helper (GPU) --type=gpu-process --user-data-dir=/Users/huazhou/Library/Application Support/RStudio --gpu-preferences=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 --shared-files --field-trial-handle=1718379636,r,14609628184229713530,7014257192654722631,262144 --disable-features=SpareRendererForSitePerProcess --seatbelt-client=33
  504 39732 39730   0 11:12AM ??         0:00.41 /Applications/RStudio.app/Contents/Frameworks/RStudio Helper.app/Contents/MacOS/RStudio Helper --type=utility --utility-sub-type=network.mojom.NetworkService --lang=en-US --service-sandbox-type=network --user-data-dir=/Users/huazhou/Library/Application Support/RStudio --shared-files --field-trial-handle=1718379636,r,14609628184229713530,7014257192654722631,262144 --disable-features=SpareRendererForSitePerProcess --seatbelt-client=40
  504 39747 39730   0 11:12AM ??         0:01.82 /Applications/RStudio.app/Contents/Resources/app/bin/rsession-arm64 --config-file none --program-mode desktop --www-port 27965 --launcher-token f22dc134 --show-help-home 1
  504 39750 39730   0 11:12AM ??         0:09.81 /Applications/RStudio.app/Contents/Frameworks/RStudio Helper (Renderer).app/Contents/MacOS/RStudio Helper (Renderer) --type=renderer --user-data-dir=/Users/huazhou/Library/Application Support/RStudio --app-path=/Applications/RStudio.app/Contents/Resources/app.asar --enable-sandbox --first-renderer-process --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=4 --time-ticks-at-unix-epoch=-1703506631889539 --launch-time-ticks=197737190773 --shared-files --field-trial-handle=1718379636,r,14609628184229713530,7014257192654722631,262144 --disable-features=SpareRendererForSitePerProcess --api-keys=desktopInfo|desktop|desktopMenuCallback --seatbelt-client=65
  504 39773 39747   0 11:12AM ??         0:01.41 /Applications/RStudio.app/Contents/MacOS/RStudio /Users/huazhou/.cache/rstudio/copilot/dist/agent.js
  504 39786 39747   0 11:12AM ??         0:00.50 /Applications/RStudio.app/Contents/MacOS/RStudio /Users/huazhou/.cache/rstudio/copilot/dist/agent.js
  504 39960     1   0 11:13AM ??         0:00.03 /System/Library/Frameworks/Metal.framework/Versions/A/XPCServices/MTLCompilerService.xpc/Contents/MacOS/MTLCompilerService
   89 40138     1   0 11:13AM ??         0:00.05 /System/Library/Frameworks/CoreServices.framework/Frameworks/Metadata.framework/Versions/A/Support/mdworker_shared -s mdworker -c MDSImporterWorker -m com.apple.mdworker.shared
  504 40632     1   0 11:14AM ??         0:00.08 /System/Library/Frameworks/CoreServices.framework/Frameworks/Metadata.framework/Versions/A/Support/mdworker_shared -s mdworker -c MDSImporterWorker -m com.apple.mdworker.shared
  504 40633     1   0 11:14AM ??         0:00.10 /System/Library/Frameworks/CoreServices.framework/Frameworks/Metadata.framework/Versions/A/Support/mdworker_shared -s mdworker -c MDSImporterWorker -m com.apple.mdworker.shared
  504 40647 39747   0 11:14AM ??         0:00.01 /bin/bash /Applications/quarto/bin/quarto preview linux.qmd --to html --no-watch-inputs --no-browse
  504 40656 40647   0 11:14AM ??         0:00.79 /Applications/quarto/bin/tools/deno-aarch64-apple-darwin/deno run --unstable --no-config --cached-only --allow-read --allow-write --allow-run --allow-env --allow-net --allow-ffi --no-check --importmap=/Applications/quarto/bin/vendor/import_map.json /Applications/quarto/bin/quarto.js preview linux.qmd --to html --no-watch-inputs --no-browse
  504 40657 40656   0 11:14AM ??         0:00.39 /Library/Frameworks/R.framework/Resources/bin/exec/R --no-echo --no-restore --file=/Applications/quarto/share/rmd/rmd.R
  504 40771 40657   0 11:14AM ??         0:00.00 sh -c 'bash'  -c 'ps -eaf' 2>&1
    0 40772 40771   0 11:14AM ??         0:00.00 ps -eaf
  278 57552     1   0 Mon05PM ??         0:00.09 /System/Library/PrivateFrameworks/CoreSpeech.framework/Versions/A/XPCServices/CoreSpeechXPC.xpc/Contents/MacOS/CoreSpeechXPC
  278 67318     1   0 Sun11PM ??         0:00.12 /System/Library/PrivateFrameworks/MobileAccessoryUpdater.framework/XPCServices/EAUpdaterService.xpc/Contents/MacOS/EAUpdaterService
    0 67437     1   0 Sun11PM ??         0:00.63 /Library/Application Support/Citrix Receiver/ctxworkspaceupdater
    0 69074     1   0 Sat11PM ??         0:00.03 /usr/libexec/tzd
    0 69126     1   0 Sat11PM ??         0:00.04 /System/Library/PrivateFrameworks/Noticeboard.framework/Versions/A/Resources/nbstated
    0 76120     1   0 11:02PM ??         0:00.01 /usr/libexec/periodic-wrapper weekly
  257 76137     1   0 11:02PM ??         0:00.08 /usr/libexec/DataDetectorsSourceAccess
  247 86607     1   0 Sun03AM ??         0:00.08 /System/Library/PrivateFrameworks/GameControllerFoundation.framework/Versions/A/XPCServices/GameControllerConfigService.xpc/Contents/MacOS/GameControllerConfigService
    0 86813     1   0 Sun04AM ??         0:00.03 /usr/libexec/microstackshot
    0 96520     1   0  5:02AM ??         0:29.13 /usr/libexec/PerfPowerServices
    0 38078 27225   0 11:08AM ttys000    0:00.01 login -pf huazhou
  504 38079 38078   0 11:08AM ttys000    0:00.04 -zsh

• All Python processes:

ps -eaf | grep python

  504 27688 27537   0  9:51AM ??         0:00.03 /Applications/Box.app/Contents/MacOS/python -B -c from multiprocessing.resource_tracker import main;main(31)
  504 40773 40657   0 11:14AM ??         0:00.00 sh -c 'bash'  -c 'ps -eaf | grep python' 2>&1
  504 40774 40773   0 11:14AM ??         0:00.00 bash -c ps -eaf | grep python
  504 40776 40774   0 11:14AM ??         0:00.00 grep python

• Process with PID=1:

ps -fp 1

  UID   PID  PPID   C STIME   TTY           TIME CMD
    0     1     0   0 Sat10AM ??        51:33.10 /sbin/launchd

• All processes owned by a user:

ps -fu $USER

  UID   PID  PPID   C STIME   TTY           TIME CMD
  504  1176     1   0 Sat11AM ??        44:09.87 /usr/sbin/distnoted agent
  504  1225     1   0 Sat11AM ??         1:34.97 /usr/sbin/cfprefsd agent
  504  1254     1   0 Sat11AM ??         0:36.62 /usr/libexec/lsd
  504  1288     1   0 Sat11AM ??         0:00.02 /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/XPCServices/csnameddatad.xpc/Contents/MacOS/csnameddatad
  504  1317     1   0 Sat11AM ??         2:35.39 /usr/libexec/trustd --agent
  504  1330     1   0 Sat11AM ??         0:19.67 /System/Library/Frameworks/CoreServices.framework/Frameworks/Metadata.framework/Versions/A/Support/mdbulkimport -s mdworker-bundle -c MDSImporterBundleFinder -m com.apple.metadata.mdbulkimport
  504  1592     1   0 Sat11AM ??         0:09.51 /usr/libexec/pkd
  504  2026     1   0 Sat11AM ??         0:00.64 /System/Library/Frameworks/Security.framework/Versions/A/XPCServices/TrustedPeersHelper.xpc/Contents/MacOS/TrustedPeersHelper
  504  2058     1   0 Sat11AM ??         0:18.31 /usr/libexec/secinitd
  504  2072     1   0 Sat11AM ??         0:11.40 /usr/libexec/containermanagerd --runmode=agent --user-container-mode=current --bundle-container-mode=proxy --system-container-mode=none
  504  2077     1   0 Sat11AM ??         0:03.78 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/XPCServices/com.apple.hiservices-xpcservice.xpc/Contents/MacOS/com.apple.hiservices-xpcservice
  504  2080     1   0 Sat11AM ??         0:01.41 /System/Library/Frameworks/CryptoTokenKit.framework/ctkd -tw
  504  2082     1   0 Sat11AM ??         0:01.24 /System/Library/Frameworks/LocalAuthentication.framework/Support/coreauthd
  504  2111     1   0 Sat11AM ??         0:10.27 /System/Library/PrivateFrameworks/GeoServices.framework/Versions/A/XPCServices/com.apple.geod.xpc/Contents/MacOS/com.apple.geod
  504  2199     1   0 Sat11AM ??         0:00.01 /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/DictionaryServices.framework/Versions/A/XPCServices/com.apple.DictionaryServiceHelper.xpc/Contents/MacOS/com.apple.DictionaryServiceHelper
  504  2207     1   0 Sat11AM ??         0:01.30 /System/Library/PrivateFrameworks/ContextKit.framework/Versions/A/XPCServices/ContextService.xpc/Contents/MacOS/ContextService
  504  2411     1   0 Sat11AM ??         0:00.32 /System/Library/PrivateFrameworks/CloudPhotoServices.framework/Versions/A/XPCServices/com.apple.CloudPhotosConfiguration.xpc/Contents/MacOS/com.apple.CloudPhotosConfiguration
  504  2457     1   0 Sat11AM ??         1:21.25 /System/Library/PrivateFrameworks/TextInputUIMacHelper.framework/Versions/A/XPCServices/CursorUIViewService.xpc/Contents/MacOS/CursorUIViewService
  504  2644     1   0 Sat11AM ??         0:00.17 /System/Library/Frameworks/MediaAccessibility.framework/Versions/A/XPCServices/com.apple.accessibility.mediaaccessibilityd.xpc/Contents/MacOS/com.apple.accessibility.mediaaccessibilityd
  504  4262     1   0 Sat11AM ??         0:00.04 /System/Library/PrivateFrameworks/PodcastServices.framework/XPCServices/PodcastContentService.xpc/Contents/MacOS/PodcastContentService
  504  4264     1   0 Sat11AM ??         0:00.05 /System/Library/PrivateFrameworks/BookKit.framework/Versions/A/XPCServices/com.apple.BKAgentService.xpc/Contents/MacOS/com.apple.BKAgentService
  504 18172     1   0 Sat11AM ??         0:00.02 /System/Library/PrivateFrameworks/ToneLibrary.framework/Versions/A/XPCServices/com.apple.tonelibraryd.xpc/Contents/MacOS/com.apple.tonelibraryd
  504 20950     1   0 Sat12PM ??         0:00.11 /System/Library/PrivateFrameworks/DistributedEvaluation.framework/Versions/A/XPCServices/com.apple.siri-distributed-evaluation.xpc/Contents/MacOS/com.apple.siri-distributed-evaluation
  504 26870     1   0  9:51AM ??         0:04.32 /Library/Application Support/Adobe/Adobe Desktop Common/IPCBox/AdobeIPCBroker.app/Contents/MacOS/AdobeIPCBroker -launchedbyvulcan /Applications/Utilities/Adobe Creative Cloud/ACC/Creative Cloud.app/Contents/MacOS/Creative Cloud
  504 26871     1   0  9:51AM ??         0:04.11 /System/Library/PrivateFrameworks/FileProvider.framework/Support/fileproviderd
  504 27188     1   0  9:51AM ??         0:01.25 /usr/libexec/UserEventAgent (Aqua)
  504 27190     1   0  9:51AM ??         0:00.38 /usr/libexec/bluetoothuserd
  504 27192     1   0  9:51AM ??         0:01.88 /System/Library/CoreServices/ControlCenter.app/Contents/MacOS/ControlCenter
  504 27193     1   0  9:51AM ??         0:04.74 /System/Library/PrivateFrameworks/CoreDuetContext.framework/Resources/ContextStoreAgent
  504 27194     1   0  9:51AM ??         0:00.20 /System/Library/CoreServices/CoreServicesUIAgent.app/Contents/MacOS/CoreServicesUIAgent
  504 27195     1   0  9:51AM ??         0:00.48 /usr/sbin/universalaccessd launchd -s
  504 27196     1   0  9:51AM ??         0:00.02 /System/Library/PrivateFrameworks/CloudServices.framework/Helpers/com.apple.sbd
  504 27199     1   0  9:51AM ??         0:00.15 /System/Library/PrivateFrameworks/BackgroundTaskManagement.framework/Support/BackgroundTaskManagementAgent.app/Contents/MacOS/BackgroundTaskManagementAgent
  504 27200     1   0  9:51AM ??         0:00.08 /System/Library/PrivateFrameworks/UserNotificationsCore.framework/Support/usernotificationsd
  504 27201     1   0  9:51AM ??         0:02.05 /usr/libexec/ContinuityCaptureAgent server
  504 27202     1   0  9:51AM ??         0:01.50 /System/Library/Frameworks/Accounts.framework/Versions/A/Support/accountsd
  504 27203     1   0  9:51AM ??         0:00.02 /System/Library/PrivateFrameworks/CoreFollowUp.framework/Versions/A/Support/followupd
  504 27204     1   0  9:51AM ??         0:00.71 /System/Library/PrivateFrameworks/VoiceShortcuts.framework/Versions/A/Support/siriactionsd
  504 27205     1   0  9:51AM ??         0:00.39 /System/Library/PrivateFrameworks/SyncedDefaults.framework/Support/syncdefaultsd
  504 27206     1   0  9:51AM ??         0:00.45 /usr/sbin/usernoted
  504 27207     1   0  9:51AM ??         0:00.21 /System/Library/CoreServices/CoreLocationAgent.app/Contents/MacOS/CoreLocationAgent
  504 27208     1   0  9:51AM ??         0:00.65 /System/Library/PrivateFrameworks/CalendarDaemon.framework/Support/calaccessd
  504 27209     1   0  9:51AM ??         0:00.28 /usr/libexec/pboard
  504 27210     1   0  9:51AM ??         3:24.10 /Applications/Google Chrome.app/Contents/MacOS/Google Chrome
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  504 27271 27210   0  9:51AM ??         0:32.27 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper.app/Contents/MacOS/Google Chrome Helper --type=utility --utility-sub-type=network.mojom.NetworkService --lang=en-US --service-sandbox-type=network --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=27
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  504 27299 27210   0  9:51AM ??         0:03.15 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper (Renderer).app/Contents/MacOS/Google Chrome Helper (Renderer) --type=renderer --extension-process --origin-trial-disabled-features=WebGPU --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=6 --time-ticks-at-unix-epoch=-1703506631900517 --launch-time-ticks=192874228792 --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=80
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  504 27312 27210   0  9:51AM ??         0:06.65 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper (Renderer).app/Contents/MacOS/Google Chrome Helper (Renderer) --type=renderer --extension-process --origin-trial-disabled-features=WebGPU --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=11 --time-ticks-at-unix-epoch=-1703506631900517 --launch-time-ticks=192874410539 --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=80
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  504 27342 27212   0  9:51AM ??         0:00.00 <defunct>
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  504 28993 27210   0  9:55AM ??         0:03.44 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper (Renderer).app/Contents/MacOS/Google Chrome Helper (Renderer) --type=renderer --origin-trial-disabled-features=WebGPU --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=33 --time-ticks-at-unix-epoch=-1703506631900517 --launch-time-ticks=193088492043 --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=636
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  504 31229     1   0 10:06AM ??         0:00.01 /System/Library/Frameworks/NetFS.framework/Versions/A/XPCServices/PlugInLibraryService.xpc/Contents/MacOS/PlugInLibraryService
  504 31241 27210   0 10:07AM ??         0:06.99 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper (Renderer).app/Contents/MacOS/Google Chrome Helper (Renderer) --type=renderer --origin-trial-disabled-features=WebGPU --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=39 --time-ticks-at-unix-epoch=-1703506631900517 --launch-time-ticks=193797381126 --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=192
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  504 31515     1   0 10:10AM ??         0:00.76 /System/Library/Frameworks/Metal.framework/Versions/A/XPCServices/MTLCompilerService.xpc/Contents/MacOS/MTLCompilerService
  504 33002     1   0 10:27AM ??         0:43.24 /Applications/WeChat.app/Contents/MacOS/WeChat
  504 33006 33002   0 10:27AM ??         0:07.16 /Applications/WeChat.app/Contents/MacOS/WeChatAppEx.app/Contents/MacOS/WeChatAppEx --log-level=2 --lang=en --wechat-files-path=/Users/huazhou/Library/Containers/com.tencent.xinWeChat/Data/.wxapplet --no-codecache --product-id=1000 --wechat-sub-user-agent=MicroMessenger/6.8.0(0x16080000) MacWechat/3.8.5(0x13080510) --appshim-flags=7 --client_version=319292688 --bundle-id=5A4RE8SF68.com.tencent.xinWeChat --wmpf-mojo-handle=3362559639
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  504 33009 33006   0 10:28AM ??         0:29.81 /Applications/WeChat.app/Contents/MacOS/WeChatAppEx.app/Contents/Frameworks/WeChatAppEx Framework.framework/Versions/C/Helpers/WeChatAppEx Helper (GPU).app/Contents/MacOS/WeChatAppEx Helper (GPU) --type=gpu-process --log-level=2 --client_version=319292688 --bundle-id=5A4RE8SF68.com.tencent.xinWeChat --product-id=1000 --gpu-preferences=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 --log-level=2 --shared-files --field-trial-handle=1718379636,r,16995014633199079317,6298364114720810509,131072 --enable-features=NetworkServiceMemoryCache,OverlayScrollbar,WebPredictor,kXWorker --disable-features=AnonymousIframeOriginTrial,AudioServiceOutOfProcess,AutoupgradeMixedContent,BackForwardCache,DigitalGoodsApi,NotificationTriggers,PeriodicBackgroundSync,Portals,TFLiteLanguageDetectionEnabled,Vulkan,WebOTP --seatbelt-client=17
  504 33010     1   0 10:28AM ??         0:03.40 /System/Library/Frameworks/VideoToolbox.framework/Versions/A/XPCServices/VTDecoderXPCService.xpc/Contents/MacOS/VTDecoderXPCService
  504 33017 33006   0 10:28AM ??         0:00.89 /Applications/WeChat.app/Contents/MacOS/WeChatAppEx.app/Contents/Frameworks/WeChatAppEx Framework.framework/Versions/C/Helpers/WeChatAppEx Helper.app/Contents/MacOS/WeChatAppEx Helper --type=utility --utility-sub-type=flue.mojom.ILinkServiceHost --lang=en --service-sandbox-type=none --use-mock-keychain --log-level=2 --client_version=319292688 --bundle-id=5A4RE8SF68.com.tencent.xinWeChat --product-id=1000 --log-level=2 --shared-files --field-trial-handle=1718379636,r,16995014633199079317,6298364114720810509,131072 --enable-features=NetworkServiceMemoryCache,OverlayScrollbar,WebPredictor,kXWorker --disable-features=AnonymousIframeOriginTrial,AudioServiceOutOfProcess,AutoupgradeMixedContent,BackForwardCache,DigitalGoodsApi,NotificationTriggers,PeriodicBackgroundSync,Portals,TFLiteLanguageDetectionEnabled,Vulkan,WebOTP
  504 33018 33006   0 10:28AM ??         0:01.02 /Applications/WeChat.app/Contents/MacOS/WeChatAppEx.app/Contents/Frameworks/WeChatAppEx Framework.framework/Versions/C/Helpers/WeChatAppEx Helper (Renderer).app/Contents/MacOS/WeChatAppEx Helper (Renderer) --type=renderer --client_version=319292688 --bundle-id=5A4RE8SF68.com.tencent.xinWeChat --wmpf-render-type=6 --product-id=1000 --first-renderer-process --disable-notifications --log-level=2 --lang=en --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=5 --time-ticks-at-unix-epoch=-1703506631859661 --launch-time-ticks=195059058696 --shared-files --field-trial-handle=1718379636,r,16995014633199079317,6298364114720810509,131072 --enable-features=NetworkServiceMemoryCache,OverlayScrollbar,WebPredictor,kXWorker --disable-features=AnonymousIframeOriginTrial,AudioServiceOutOfProcess,AutoupgradeMixedContent,BackForwardCache,DigitalGoodsApi,NotificationTriggers,PeriodicBackgroundSync,Portals,TFLiteLanguageDetectionEnabled,Vulkan,WebOTP --seatbelt-client=43
  504 33032     1   0 10:28AM ??         0:00.17 /System/Library/Frameworks/WebKit.framework/Versions/A/XPCServices/com.apple.WebKit.WebContent.xpc/Contents/MacOS/com.apple.WebKit.WebContent
  504 33033     1   0 10:28AM ??         0:00.02 /System/Library/Frameworks/AudioToolbox.framework/XPCServices/com.apple.audio.SandboxHelper.xpc/Contents/MacOS/com.apple.audio.SandboxHelper
  504 33034     1   0 10:28AM ??         0:00.06 /System/Library/Frameworks/WebKit.framework/Versions/A/XPCServices/com.apple.WebKit.Networking.xpc/Contents/MacOS/com.apple.WebKit.Networking
  504 33143     1   0 10:28AM ??         0:00.56 /System/Library/Frameworks/AppKit.framework/Versions/C/XPCServices/com.apple.appkit.xpc.openAndSavePanelService.xpc/Contents/MacOS/com.apple.appkit.xpc.openAndSavePanelService
  504 33147     1   0 10:28AM ??         0:00.10 /System/Library/Frameworks/QuickLookUI.framework/Versions/A/XPCServices/QuickLookUIService.xpc/Contents/MacOS/QuickLookUIService
  504 33901     1   0 10:36AM ??         0:01.45 /System/Library/Frameworks/AppKit.framework/Versions/C/XPCServices/com.apple.appkit.xpc.openAndSavePanelService.xpc/Contents/MacOS/com.apple.appkit.xpc.openAndSavePanelService
  504 33902     1   0 10:36AM ??         0:00.09 /System/Library/Frameworks/QuickLookUI.framework/Versions/A/XPCServices/QuickLookUIService.xpc/Contents/MacOS/QuickLookUIService
  504 34032     1   0 10:38AM ??         0:03.27 /System/Library/Input Methods/SCIM.app/Contents/PlugIns/SCIM_Extension.appex/Contents/MacOS/SCIM_Extension -AppleLanguages ("en-US", "zh-Hans-US")
  504 34196 27210   0 10:39AM ??         0:00.92 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper (Renderer).app/Contents/MacOS/Google Chrome Helper (Renderer) --type=renderer --origin-trial-disabled-features=WebGPU --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=155 --time-ticks-at-unix-epoch=-1703506631900517 --launch-time-ticks=195711088112 --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=230
  504 34197     1   0 10:39AM ??         0:00.05 /usr/libexec/mlruntimed
  504 34837     1   0 10:41AM ??         0:00.56 /System/Library/Frameworks/VideoToolbox.framework/Versions/A/XPCServices/VTEncoderXPCService.xpc/Contents/MacOS/VTEncoderXPCService
  504 34843     1   0 10:41AM ??         0:00.02 /System/Library/Frameworks/AudioToolbox.framework/XPCServices/com.apple.audio.SandboxHelper.xpc/Contents/MacOS/com.apple.audio.SandboxHelper
  504 34844     1   0 10:41AM ??         0:00.14 /System/Library/Frameworks/VideoToolbox.framework/Versions/A/XPCServices/VTDecoderXPCService.xpc/Contents/MacOS/VTDecoderXPCService
  504 37489 27210   0 11:01AM ??         0:01.56 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper (Renderer).app/Contents/MacOS/Google Chrome Helper (Renderer) --type=renderer --origin-trial-disabled-features=WebGPU --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=223 --time-ticks-at-unix-epoch=-1703506631900517 --launch-time-ticks=197064686007 --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=192
  504 37513     1   0 11:02AM ??         0:00.02 /System/Library/Frameworks/AudioToolbox.framework/XPCServices/com.apple.audio.SandboxHelper.xpc/Contents/MacOS/com.apple.audio.SandboxHelper
  504 37514     1   0 11:02AM ??         0:00.81 /System/Library/Frameworks/VideoToolbox.framework/Versions/A/XPCServices/VTEncoderXPCService.xpc/Contents/MacOS/VTEncoderXPCService
  504 37515     1   0 11:02AM ??         0:00.01 /System/Library/Frameworks/AudioToolbox.framework/XPCServices/com.apple.audio.SandboxHelper.xpc/Contents/MacOS/com.apple.audio.SandboxHelper
  504 37516     1   0 11:02AM ??         0:00.11 /System/Library/CoreServices/OSDUIHelper.app/Contents/MacOS/OSDUIHelper
  504 37566 27210   0 11:02AM ??         0:03.96 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper (Renderer).app/Contents/MacOS/Google Chrome Helper (Renderer) --type=renderer --origin-trial-disabled-features=WebGPU --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=225 --time-ticks-at-unix-epoch=-1703506631900517 --launch-time-ticks=197137199414 --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=192
  504 38096 27210   0 11:08AM ??         0:00.06 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper.app/Contents/MacOS/Google Chrome Helper --type=utility --utility-sub-type=data_decoder.mojom.DataDecoderService --lang=en-US --service-sandbox-type=service --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=192
  504 38103 27210   0 11:08AM ??         0:01.94 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper (Renderer).app/Contents/MacOS/Google Chrome Helper (Renderer) --type=renderer --origin-trial-disabled-features=WebGPU --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=237 --time-ticks-at-unix-epoch=-1703506631900517 --launch-time-ticks=197469685778 --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=192
  504 38108 27210   0 11:08AM ??         0:00.54 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper (Renderer).app/Contents/MacOS/Google Chrome Helper (Renderer) --type=renderer --origin-trial-disabled-features=WebGPU --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=238 --time-ticks-at-unix-epoch=-1703506631900517 --launch-time-ticks=197472588096 --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=211
  504 38127 27210   0 11:08AM ??         0:01.81 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper (Renderer).app/Contents/MacOS/Google Chrome Helper (Renderer) --type=renderer --origin-trial-disabled-features=WebGPU --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=250 --time-ticks-at-unix-epoch=-1703506631900517 --launch-time-ticks=197495431472 --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=192
  504 38166 27210   0 11:08AM ??         0:00.05 /Applications/Google Chrome.app/Contents/Frameworks/Google Chrome Framework.framework/Versions/120.0.6099.129/Helpers/Google Chrome Helper (Renderer).app/Contents/MacOS/Google Chrome Helper (Renderer) --type=renderer --origin-trial-disabled-features=WebGPU --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=251 --time-ticks-at-unix-epoch=-1703506631900517 --launch-time-ticks=197496407844 --shared-files --field-trial-handle=1718379636,r,6742120930418319793,9150852737802887181,262144 --variations-seed-version=20231218-080113.411000 --seatbelt-client=211
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  504 39731 39730   0 11:12AM ??         0:01.74 /Applications/RStudio.app/Contents/Frameworks/RStudio Helper (GPU).app/Contents/MacOS/RStudio Helper (GPU) --type=gpu-process --user-data-dir=/Users/huazhou/Library/Application Support/RStudio --gpu-preferences=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 --shared-files --field-trial-handle=1718379636,r,14609628184229713530,7014257192654722631,262144 --disable-features=SpareRendererForSitePerProcess --seatbelt-client=33
  504 39732 39730   0 11:12AM ??         0:00.41 /Applications/RStudio.app/Contents/Frameworks/RStudio Helper.app/Contents/MacOS/RStudio Helper --type=utility --utility-sub-type=network.mojom.NetworkService --lang=en-US --service-sandbox-type=network --user-data-dir=/Users/huazhou/Library/Application Support/RStudio --shared-files --field-trial-handle=1718379636,r,14609628184229713530,7014257192654722631,262144 --disable-features=SpareRendererForSitePerProcess --seatbelt-client=40
  504 39747 39730   0 11:12AM ??         0:01.83 /Applications/RStudio.app/Contents/Resources/app/bin/rsession-arm64 --config-file none --program-mode desktop --www-port 27965 --launcher-token f22dc134 --show-help-home 1
  504 39750 39730   0 11:12AM ??         0:09.82 /Applications/RStudio.app/Contents/Frameworks/RStudio Helper (Renderer).app/Contents/MacOS/RStudio Helper (Renderer) --type=renderer --user-data-dir=/Users/huazhou/Library/Application Support/RStudio --app-path=/Applications/RStudio.app/Contents/Resources/app.asar --enable-sandbox --first-renderer-process --lang=en-US --num-raster-threads=4 --enable-zero-copy --enable-gpu-memory-buffer-compositor-resources --enable-main-frame-before-activation --renderer-client-id=4 --time-ticks-at-unix-epoch=-1703506631889539 --launch-time-ticks=197737190773 --shared-files --field-trial-handle=1718379636,r,14609628184229713530,7014257192654722631,262144 --disable-features=SpareRendererForSitePerProcess --api-keys=desktopInfo|desktop|desktopMenuCallback --seatbelt-client=65
  504 39773 39747   0 11:12AM ??         0:01.41 /Applications/RStudio.app/Contents/MacOS/RStudio /Users/huazhou/.cache/rstudio/copilot/dist/agent.js
  504 39786 39747   0 11:12AM ??         0:00.50 /Applications/RStudio.app/Contents/MacOS/RStudio /Users/huazhou/.cache/rstudio/copilot/dist/agent.js
  504 39960     1   0 11:13AM ??         0:00.03 /System/Library/Frameworks/Metal.framework/Versions/A/XPCServices/MTLCompilerService.xpc/Contents/MacOS/MTLCompilerService
  504 40632     1   0 11:14AM ??         0:00.08 /System/Library/Frameworks/CoreServices.framework/Frameworks/Metadata.framework/Versions/A/Support/mdworker_shared -s mdworker -c MDSImporterWorker -m com.apple.mdworker.shared
  504 40633     1   0 11:14AM ??         0:00.10 /System/Library/Frameworks/CoreServices.framework/Frameworks/Metadata.framework/Versions/A/Support/mdworker_shared -s mdworker -c MDSImporterWorker -m com.apple.mdworker.shared
  504 40647 39747   0 11:14AM ??         0:00.01 /bin/bash /Applications/quarto/bin/quarto preview linux.qmd --to html --no-watch-inputs --no-browse
  504 40656 40647   0 11:14AM ??         0:00.79 /Applications/quarto/bin/tools/deno-aarch64-apple-darwin/deno run --unstable --no-config --cached-only --allow-read --allow-write --allow-run --allow-env --allow-net --allow-ffi --no-check --importmap=/Applications/quarto/bin/vendor/import_map.json /Applications/quarto/bin/quarto.js preview linux.qmd --to html --no-watch-inputs --no-browse
  504 40657 40656   0 11:14AM ??         0:00.41 /Library/Frameworks/R.framework/Resources/bin/exec/R --no-echo --no-restore --file=/Applications/quarto/share/rmd/rmd.R
  504 40779 40657   0 11:14AM ??         0:00.00 sh -c 'bash'  -c 'ps -fu $USER' 2>&1
    0 40780 40779   0 11:14AM ??         0:00.00 ps -fu huazhou
    0 38078 27225   0 11:08AM ttys000    0:00.01 login -pf huazhou
  504 38079 38078   0 11:08AM ttys000    0:00.04 -zsh

8.3 Kill processes

• Kill process with PID=1001:

```{bash}
#| eval: false
kill 1001
```

• Kill all R processes.

```{bash}
#| eval: false
killall -r R
```

8.4 top

• top prints realtime process information (very useful).

```{bash}
#| eval: false
top
```

• Exit the top program by pressing the q key.

9 Secure shell (SSH)

9.1 SSH

SSH (secure shell) is the dominant cryptographic network protocol for secure network connection via an insecure network.

• On Linux or Mac Terminal, access a Linux machine by

```{bash}
#| eval: false
ssh [USERNAME]@[IP_ADDRESS]
```

Replace above [USERNAME] by your account user name on the Linux machine and [IP_ADDRESS] by the machine’s ip address. For example, to connect to the Hoffman2 cluster at UCLA

```{bash}
#| eval: false
ssh huazhou@hoffman2.idre.ucla.edu
```

• For Windows users, there are at least three ways: (1) (recommended) Git Bash which is included in Git for Windows, (2) (not recommended) PuTTY program (free), or (3) (highly recommended) use WSL for Windows to install a full fledged Linux system within Windows.

9.2 Advantages of keys over password

• Key authentication is more secure than password. Most passwords are weak.

• Script or a program may need to systematically SSH into other machines.

• Log into multiple machines using the same key.

• Seamless use of many services: Git/GitHub, AWS or Google cloud service, parallel computing on multiple hosts, Travis CI (continuous integration) etc.

• Many servers only allow key authentication and do not accept password authentication.

9.3 Key authentication

• Public key. Put on the machine(s) you want to log in.

• Private key. Put on your own computer. Consider this as the actual key in your pocket; never give private keys to others.

• Messages from server to your computer is encrypted with your public key. It can only be decrypted using your private key.

• Messages from your computer to server is signed with your private key (digital signatures) and can be verified by anyone who has your public key (authentication).

9.4 Steps to generate keys

• On Linux, Mac, or Windows Git Bash, to generate a key pair:

ssh-keygen -t rsa -f ~/.ssh/[KEY_FILENAME] -C [USERNAME]

• • [KEY_FILENAME] is the name that you want to use for your SSH key files. For example, a filename of id_rsa generates a private key file named id_rsa and a public key file named id_rsa.pub.

  • [USERNAME] is the user for whom you will apply this SSH key.

  • Use a (optional) paraphrase different from password.

• Set correct permissions on the .ssh folder and key files.
  • The permission for the ~/.ssh folder should be 700 (drwx------).
  • The permission of the private key ~/.ssh/id_rsa should be 600 (-rw-------).
  • The permission of the public key ~/.ssh/id_rsa.pub should be 644 (-rw-r--r--).

chmod 700 ~/.ssh
chmod 600 ~/.ssh/[KEY_FILENAME]
chmod 644 ~/.ssh/[KEY_FILENAME].pub

Note Windows is different, it doesn't allow change of permissions.

• Append the public key to the ~/.ssh/authorized_keys file of any Linux machine we want to SSH to, e.g.,

ssh-copy-id -i ~/.ssh/[KEY_FILENAME] [USERNAME]@[IP_ADDRESS]

Make sure the permission of the authorized_keys file is 600 (-rw-------).

• Test your new key.

ssh -i ~/.ssh/[KEY_FILENAME] [USERNAME]@[IP_ADDRESS]

• From now on, you don’t need password each time you connect from your machine to the teaching server.

• If you set paraphrase when generating keys, you’ll be prompted for the paraphrase each time the private key is used. Avoid repeatedly entering the paraphrase by using ssh-agent on Linux/Mac or Pagent on Windows.

• Same key pair can be used between any two machines. We don’t need to regenerate keys for each new connection.

9.5 Transfer files between machines

• scp securely transfers files between machines using SSH.

## copy file from local to remote
scp [LOCALFILE] [USERNAME]@[IP_ADDRESS]:/[PATH_TO_FOLDER]

## copy file from remote to local
scp [USERNAME]@[IP_ADDRESS]:/[PATH_TO_FILE] [PATH_TO_LOCAL_FOLDER]

• sftp is FTP via SSH.

• Globus is GUI program for securely transferring files between machines. To use Globus you will have to go to https://www.globus.org/ and login through UCLA by selecting your existing organizational login as UCLA. Then you will need to download their Globus Connect Personal software, then set your laptop as an endpoint. Very detailed instructions can be found at https://www.hoffman2.idre.ucla.edu/file-transfer/globus/.

• GUIs for Windows (WinSCP) or Mac (Cyberduck).

• You can even use RStudio to upload files to a remote machine with RStudio Server installed.

• (Preferred way) Use a version control system (git, svn, cvs, …) to sync project files between different machines and systems.

9.6 Line breaks in text files

• Windows uses a pair of CR and LF for line breaks.

• Linux/Unix uses an LF character only.

• MacOS X also uses a single LF character. But old Mac OS used a single CR character for line breaks.

• If transferred in binary mode (bit by bit) between OSs, a text file could look a mess.

• Most transfer programs automatically switch to text mode when transferring text files and perform conversion of line breaks between different OSs; but I used to run into problems using WinSCP. Sometimes you have to tell WinSCP explicitly a text file is being transferred.

10 Run R in Linux

10.1 Interactive mode

• Start R in the interactive mode by typing R in shell.

• Then run R script by

source("script.R")

10.2 Batch mode

• Demo script meanEst.R implements an (terrible) estimator of mean \[ {\widehat \mu}_n = \frac{\sum_{i=1}^n x_i 1_{i \text{ is prime}}}{\sum_{i=1}^n 1_{i \text{ is prime}}}. \]

cat meanEst.R

## check if a given integer is prime
isPrime = function(n) {
  if (n <= 3) {
    return (TRUE)
  }
  if (any((n %% 2:floor(sqrt(n))) == 0)) {
    return (FALSE)
  }
  return (TRUE)
}

## estimate mean only using observation with prime indices
estMeanPrimes = function (x) {
  n = length(x)
  ind = sapply(1:n, isPrime)
  return (mean(x[ind]))
}

print(estMeanPrimes(rnorm(100000)))

• To run your R code non-interactively aka in batch mode, we have at least two options:

#! eval: false
# default output to meanEst.Rout
R CMD BATCH meanEst.R

or

# output to stdout
Rscript meanEst.R

• Typically automate batch calls using a scripting language, e.g., Python, Perl, and shell script.

10.3 Pass arguments to R scripts

• Specify arguments in R CMD BATCH:

R CMD BATCH '--args mu=1 sig=2 kap=3' script.R

• Specify arguments in Rscript:

Rscript script.R mu=1 sig=2 kap=3

• Parse command line arguments using magic formula

for (arg in commandArgs(TRUE)) {
  eval(parse(text=arg))
}

in R script. After calling the above code, all command line arguments will be available in the global namespace.

• To understand the magic formula commandArgs, run R by:

R '--args mu=1 sig=2 kap=3'

and then issue commands in R

commandArgs()
commandArgs(TRUE)

• Understand the magic formula parse and eval:

rm(list = ls())
print(x)
parse(text = "x=3")
eval(parse(text = "x=3"))
print(x)

• runSim.R has components: (1) command argument parser, (2) method implementation, (3) data generator with unspecified parameter n, and (4) estimation based on generated data.

## parsing command arguments
for (arg in commandArgs(TRUE)) {
  eval(parse(text=arg))
}

## check if a given integer is prime
isPrime = function(n) {
  if (n <= 3) {
    return (TRUE)
  }
  if (any((n %% 2:floor(sqrt(n))) == 0)) {
    return (FALSE)
  }
  return (TRUE)
}

## estimate mean only using observation with prime indices
estMeanPrimes = function (x) {
  n = length(x)
  ind = sapply(1:n, isPrime)
  return (mean(x[ind]))
}

# simulate data
x = rnorm(n)

# estimate mean
estMeanPrimes(x)

• Call runSim.R with sample size n=100:

R CMD BATCH '--args n=100' runSim.R

or

Rscript runSim.R n=100

[1] 0.01479823

10.4 Run long jobs

• Many statistical computing tasks take long: simulation, MCMC, etc. If we exit Linux when the job is unfinished, the job is killed.

• nohup command in Linux runs program(s) immune to hangups and writes output to nohup.out by default. Logging out will not kill the process; we can log in later to check status and results.

• nohup is POSIX standard thus available on Linux and MacOS.

• Run runSim.R in background and writes output to nohup.out:

nohup Rscript runSim.R n=100 &

[1] -0.1064923

The & at the end of the command instructs Linux to run this command in background, so we gain control of the terminal immediately.

10.5 screen

• screen is another popular utility, but not installed by default.

• Typical workflow using screen.

  0. Access remote server using ssh.

  1. Start jobs in batch mode.

  2. Detach jobs.

  3. Exit from server, wait for jobs to finish.

  4. Access remote server using ssh.

  5. Re-attach jobs, check on progress, get results, etc.

10.6 Use R to call R

R in conjunction with nohup (or screen) can be used to orchestrate a large simulation study.

• It can be more elegant, transparent, and robust to parallelize jobs corresponding to different scenarios (e.g., different generative models) outside of the code used to do statistical computation.

• We consider a simulation study in R but the same approach could be used with code written in Julia, Matlab, Python, etc.

• Python in many ways makes a better glue.

• Suppose we have

  • runSim.R which runs a simulation based on command line argument n.
    
  • A large collection of n values that we want to use in our simulation study.
    
  • Access to a server with 128 cores.
    How to parallelize the job?

• Option 1: manually call runSim.R for each setting.

• Option 2 (smarter): automate calls using R and nohup.

• Let’s demonstrate using the script autoSim.R

cat autoSim.R

# autoSim.R

nVals <- seq(100, 1000, by=100)
for (n in nVals) {
  oFile <- paste("n", n, ".txt", sep="")
  sysCall <- paste("nohup Rscript runSim.R n=", n, " > ", oFile, sep="")
  system(sysCall, wait = FALSE)
  print(paste("sysCall=", sysCall, sep=""))
}

Note when we call bash command using the system function in R, we set optional argument wait=FALSE so that jobs can be run parallel.

Rscript autoSim.R

[1] "sysCall=nohup Rscript runSim.R n=100 > n100.txt"
[1] "sysCall=nohup Rscript runSim.R n=200 > n200.txt"
[1] "sysCall=nohup Rscript runSim.R n=300 > n300.txt"
[1] "sysCall=nohup Rscript runSim.R n=400 > n400.txt"
[1] "sysCall=nohup Rscript runSim.R n=500 > n500.txt"
[1] "sysCall=nohup Rscript runSim.R n=600 > n600.txt"
[1] "sysCall=nohup Rscript runSim.R n=700 > n700.txt"
[1] "sysCall=nohup Rscript runSim.R n=800 > n800.txt"
[1] "sysCall=nohup Rscript runSim.R n=900 > n900.txt"
[1] "sysCall=nohup Rscript runSim.R n=1000 > n1000.txt"

• Now we just need to write a script to collect results from the output files.

• Later we will learn how to coordinate large scale computation on UCLA Hoffman2 cluster, using Linux and R scripting.

11 Some other Linux commands

• Log out Linux: exit or logout or ctrl+d.

• Clear screen: clear.